gromacs →
2021.4-2 →
armhf → 2021-11-11 11:01:49
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| gromacs 2021.4-2 (armhf) Thu, 11 Nov 2021 08:05:06 +0000 |
+==============================================================================+
Package: gromacs
Version: 2021.4-2
Source Version: 2021.4-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-06ca5669-57a1-4002-8b02-c74c30947249' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 14s (1838 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 86.6 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main gromacs 2021.4-2 (dsc) [2985 B]
Get:2 http://172.17.0.1/private bookworm-staging/main gromacs 2021.4-2 (tar) [48.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main gromacs 2021.4-2 (tar) [38.0 MB]
Get:4 http://172.17.0.1/private bookworm-staging/main gromacs 2021.4-2 (diff) [40.9 kB]
Fetched 86.6 MB in 26s (3349 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-TLdYUD/gromacs-2021.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-TLdYUD' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-M9WCO5/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-M9WCO5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-M9WCO5/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9987 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 13 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (66.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev
Filtered Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-M9WCO5/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Sources [570 B]
Get:5 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ Packages [652 B]
Fetched 2555 B in 0s (11.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake
cmake-data cpp-11 debhelper dh-autoreconf dh-elpa-helper
dh-strip-nondeterminism distro-info-data dwz emacsen-common file gcc-11
gettext gettext-base gfortran-11 groff-base ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgcc-11-dev libgfortran-11-dev
libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev
liblapack3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3
libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client po-debconf procps python3 python3-minimal
python3.9 python3.9-minimal sensible-utils x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
gcc-11-locales dh-make gcc-11-doc gettext-doc libasprintf-dev
libgettextpo-dev gfortran-11-doc libcoarrays-dev groff lrzip liblapack-doc
libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk
libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd gfortran
| fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake
cmake-data cpp-11 debhelper dh-autoreconf dh-elpa-helper
dh-strip-nondeterminism distro-info-data dwz emacsen-common file gcc-11
gettext gettext-base gfortran-11 groff-base ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgcc-11-dev libgfortran-11-dev
libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev
liblapack3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3
libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client po-debconf procps python3 python3-minimal
python3.9 python3.9-minimal sbuild-build-depends-gromacs-dummy
sensible-utils x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 134 newly installed, 0 to remove and 13 not upgraded.
Need to get 194 MB of archives.
After this operation, 770 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-M9WCO5/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1 [38.4 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1 [21.6 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1 [38.0 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.7p1-1 [882 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-5 [67.4 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.9 [11.2 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.21.4-1 [1878 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.21.4-1 [3462 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-10+rpi1 [42.3 MB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-10+rpi1 [697 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-10+rpi1 [48.3 MB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf distro-info-data all 0.52 [7596 B]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-10+rpi1 [234 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.2.0-10+rpi1 [280 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf gfortran-11 armhf 11.2.0-10+rpi1 [43.8 MB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 36.0-1 [53.2 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 36.0-1 [27.3 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 36.0-1 [60.1 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.6.0-1 [127 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.14-3 [21.8 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.14-3 [34.7 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.6.0-1 [198 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.57.02-2 [26.0 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-3 [39.9 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.6.0-1 [20.2 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 36.0-1 [186 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.1~rc5-1 [476 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.2~rc1-5+rpi1 [1779 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.2~rc1-5+rpi1 [180 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.1~rc5-1 [640 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.2~rc1-5+rpi1 [209 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.2~rc1-5+rpi1 [937 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf x11proto-dev all 2021.5-1 [599 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.7.2-2 [780 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-bin armhf 1.14 [4752 B]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-dev armhf 1.14 [5548 B]
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Setting up media-types (4.0.0) ...
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Setting up bsdextrautils (2.37.2-4) ...
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Setting up libedit2:armhf (3.1-20210910-1) ...
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Setting up gfortran-11 (11.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
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Setting up dwz (0.14-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.74.0-1.3) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up ibverbs-providers:armhf (36.0-1) ...
Setting up openssh-client (1:8.7p1-1) ...
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Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3 (3.9.7-1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (470.57.02-2) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
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Setting up cmake (3.21.4-1) ...
Setting up libhwloc-dev:armhf (2.6.0-1) ...
Setting up lsb-release (11.1.0+rpi1) ...
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Setting up debhelper (13.5.2) ...
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Setting up libfabric1 (1.11.0-2) ...
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Setting up libpmix-dev:armhf (4.1.1~rc5-1) ...
Setting up openmpi-bin (4.1.2~rc1-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.14) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.21.4-1 cmake-data_3.21.4-1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.78 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-elpa-helper_2.0.9 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 distro-info-data_0.52 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 emacsen-common_3.0.4 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-11_11.2.0-10+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 ibverbs-providers_36.0-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblas-dev_3.10.0-1 libblas3_3.10.0-1 libblkid1_2.37.2-4 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcbor0_0.5.0+dfsg-2 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl4_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.8.0-1 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran-11-dev_11.2.0-10+rpi1 libgfortran5_11.2.0-10+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhwloc-dev_2.6.0-1 libhwloc-plugins_2.6.0-1 libhwloc15_2.6.0-1 libibverbs-dev_36.0-1 libibverbs1_36.0-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui_1.12.1+dfsg-8 libjsoncpp24_1.9.4-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.10.0-1 liblapack3_3.10.0-1 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.14-3 libnuma1_2.0.14-3 libopenmpi-dev_4.1.2~rc1-5+rpi1 libopenmpi3_4.1.2~rc1-5+rpi1 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpmix-dev_4.1.1~rc5-1 libpmix2_4.1.1~rc5-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.7-1 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 librdmacm1_36.0-1 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libuv1_1.42.0-1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libx11-dev_2:1.7.2-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxnvctrl0_470.57.02-2 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-4 mpi-default-bin_1.14 mpi-default-dev_1.14 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.2~rc1-5+rpi1 openmpi-common_4.1.2~rc1-5+rpi1 openssh-client_1:8.7p1-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.7-1 python3-minimal_3.9.7-1 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 x11proto-dev_2021.5-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.L170bOh3/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 9 02:21:22 2021 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2021.4-2.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2021.4.orig.tar.gz
dpkg-source: info: unpacking gromacs_2021.4.orig-regressiontests.tar.gz
dpkg-source: info: unpacking gromacs_2021.4-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
dpkg-source: info: applying i386-disable-specific-tests.patch
dpkg-source: info: applying hppa-disable-ewaldunittest.patch
dpkg-source: info: applying manual-image-conversion.patch
dpkg-source: info: applying gammadistribution-test.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-06ca5669-57a1-4002-8b02-c74c30947249
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2021.4-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpi build-manual configure-stamp
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_INSTALL_LEGACY_API=ON )
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi" -DGMX_LIBS_SUFFIX="_mpi")
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi"
-- Using manually set library suffix: "_mpi"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- The mdrun-only build is deprecated
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpi
(mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d" -DGMX_LIBS_SUFFIX="_mpi_d")
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi_d"
-- Using manually set library suffix: "_mpi_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- The mdrun-only build is deprecated
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
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/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D PROJECT_VERSION=2021.4-Raspbian-2021.4-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2021.4-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoWithoutGit.cmake
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
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[ 3%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
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[ 3%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/manager.cpp.o -MF CMakeFiles/view_objlib.dir/view/manager.cpp.o.d -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -MF CMakeFiles/view_objlib.dir/view/molps.cpp.o.d -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF CMakeFiles/view_objlib.dir/view/popup.cpp.o.d -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/x11.cpp.o -MF CMakeFiles/view_objlib.dir/view/x11.cpp.o.d -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:77:
/<<PKGBUILDDIR>>/build/basic/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined
75 | #define HWLOC_VERSION "2.5.0"
|
In file included from /usr/include/hwloc.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:64:
/usr/include/arm-linux-gnueabihf/hwloc/autogen/config.h:15: note: this is the location of the previous definition
15 | #define HWLOC_VERSION "2.6.0"
|
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/output.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/output.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'gmx::index' {aka 'int'} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'gmx::index' {aka 'int'} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const float>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const float>, const t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<float> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const float>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function 'void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function 'real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]':
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1921 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1353:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1353 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1407:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1407 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -MF CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/options.cpp.o -MF CMakeFiles/libgromacs.dir/options/options.cpp.o.d -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -MF CMakeFiles/libgromacs.dir/options/treesupport.cpp.o.d -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
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[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
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[ 3%] Built target thread_mpi
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/3dview.cpp.o -MF CMakeFiles/view_objlib.dir/view/3dview.cpp.o.d -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -MF CMakeFiles/view_objlib.dir/view/buttons.cpp.o.d -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
[ 3%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o -MF CMakeFiles/view_objlib.dir/view/logo.cpp.o.d -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function 'void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Positions]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function 'void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Velocities]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/manager.cpp.o -MF CMakeFiles/view_objlib.dir/view/manager.cpp.o.d -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
367 | put_atoms_in_compact_unitcell(man->molw->pbcType, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -MF CMakeFiles/view_objlib.dir/view/molps.cpp.o.d -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF CMakeFiles/view_objlib.dir/view/popup.cpp.o.d -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = true]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:197:28: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
197 | relax_shell_flexcon(
| ~~~~~~~~~~~~~~~~~~~^
198 | fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | pull_work_, step == nextNSStep_, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | energyData_->enerdata(), statePropagatorData_->localNumAtoms(), x, v, box, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | hist, &forces, force_vir, mdAtoms_->mdatoms(), nrnb_, wcycle_, shellfc_, fr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | runScheduleWork_, time, energyData_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = false]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:211:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
212 | nrnb_, wcycle_, localTopology_, box, x, hist, &forces, force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
213 | mdAtoms_->mdatoms(), energyData_->enerdata(), lambda, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | energyData_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp: In member function 'void gmx::EnergyData::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp:241:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
241 | accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
242 | *inputrec_->fepvals);
| ~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/x11.cpp.o -MF CMakeFiles/view_objlib.dir/view/x11.cpp.o.d -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp: In constructor 'gmx::FreeEnergyPerturbationData::FreeEnergyPerturbationData(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:75:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
75 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:108:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
108 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::Element::_ZN3gmx19StatePropagatorData7Element24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
605 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | localStateBackup_->cg_gl, localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
609 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
610 | localStateBackup_->cg_gl, localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::Element::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:440:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
440 | mdoutf_write_to_trajectory_files(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
441 | fplog_, cr_, outf, static_cast<int>(mdof_flags), statePropagatorData_->totalNumAtoms_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | currentStep, currentTime, localStateBackup_.get(), statePropagatorData_->globalState_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | observablesHistory, statePropagatorData_->f_.view().force(), &dummyCheckpointDataHolder_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'void gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:469:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
469 | inline void ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<RVec> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'void gmx::CheckpointData<gmx::CheckpointDataOperation::Write>::arrayRef(const string&, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:485:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
485 | inline void WriteCheckpointData::arrayRef(const std::string& key, ArrayRef<const RVec> values)
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::PaddedVector<T, Allocator>::resizeWithPadding(gmx::PaddedVector<T, Allocator>::size_type) [with T = gmx::BasicVector<double>; Allocator = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'virtual void gmx::StatePropagatorData::Element::saveCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Write> >, const t_commrec*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
510 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
511 | statePropagatorData_->cgGl_, statePropagatorData_->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | statePropagatorData_->xGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
513 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | statePropagatorData_->cgGl_, statePropagatorData_->v_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | statePropagatorData_->vGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::doCheckpointData(gmx::CheckpointData<operation>*) [with gmx::CheckpointDataOperation operation = gmx::CheckpointDataOperation::Read]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::StatePropagatorData::Element::restoreCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Read> >, const t_commrec*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, bool, bool, bool, const string&, const t_inputrec*, const t_mdatoms*, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:77:
/<<PKGBUILDDIR>>/build/basic-dp/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined
75 | #define HWLOC_VERSION "2.5.0"
|
In file included from /usr/include/hwloc.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:64:
/usr/include/arm-linux-gnueabihf/hwloc/autogen/config.h:15: note: this is the location of the previous definition
15 | #define HWLOC_VERSION "2.6.0"
|
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1471:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1471 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:208:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
208 | nbnxn_atomdata_init(gmx::MDLogger(), nbv->nbat.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
209 | system.numAtomTypes, system.nonbondedParameters, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:229:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
229 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
230 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nbv->setAtomProperties(system.atomTypes, system.charges, atomInfo);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_init(const gmx::MDLogger&, nbnxn_atomdata_t*, Nbnxm::KernelType, int, int, gmx::ArrayRef<const double>, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:623:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
623 | void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:860:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
860 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:988:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
988 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1028:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1028 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1051:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1051 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1152:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1152 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1153 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_set(nbnxn_atomdata_t*, const Nbnxm::GridSet&, gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:955:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
955 | void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1410:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1410 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1411 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1405:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1405 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1173 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1287 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:215:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
215 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
216 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:135:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
135 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:222:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:446:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
446 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
447 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
448 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
449 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality, const t_forcerec*, real (*)[3], gmx::ForceWithShiftForces*, const t_mdatoms&, t_lambda*, gmx::ArrayRef<const double>, gmx_enerdata_t*, const gmx::StepWorkload&, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:458:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
458 | void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
58 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
58 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:54:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:197:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
197 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
198 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:77:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
77 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:91:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
91 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
93 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
122 | void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int> atomTypes,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:23: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
126 | nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
129 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:162:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
162 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp: In function 'std::unique_ptr<nonbonded_verlet_t> Nbnxm::init_nb_verlet(const gmx::MDLogger&, const t_inputrec*, const t_forcerec*, const t_commrec*, const gmx_hw_info_t&, bool, const gmx::DeviceStreamManager*, const gmx_mtop_t*, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp:431:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
431 | nbnxn_atomdata_init(mdlog, nbat.get(), kernelSetup.kernelType, enbnxninitcombrule, fr->ntype,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
432 | fr->nbfp, mimimumNumEnergyGroupNonbonded,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
433 | (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:233:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
233 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:279:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
279 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
292 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.numCells,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | box, calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(DDRole, MPI_Comm, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:303:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
303 | void set_ddbox_cr(DDRole ddRole,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:313:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
313 | low_set_ddbox(numPbcDimensions(ir.pbcType), inputrec2nboundeddim(&ir), dd_nc, box, true, x,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
314 | nullptr, ddbox);
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, int, int, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
231 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
308 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
309 | state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
256 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
260 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
264 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp: In function 'void dd_move_x_constraints(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void dd_move_x_constraints(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(const t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3074:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3074 | static gmx_bool test_dd_cutoff(const t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3083:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3083 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3140:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3140 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t&, const gmx_mtop_t&, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3225:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
3225 | void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t& dd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, DDRole, MPI_Comm, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:891:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
891 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:912:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
912 | set_ddbox_cr(ddRole, communicator, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:916:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
916 | set_ddbox_cr(ddRole, communicator, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2167 | dd_bonded_cg_distance(mdlog, &mtop, &ir, xGlobal, box,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2168 | options.checkBondedInteractions, &r_2b, &r_mb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3008:98: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3008 | systemInfo_, gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3053:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3053 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3061:76: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3061 | impl_(new Impl(mdlog, cr, options, mdrunOptions, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_print_missing_interactions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:364:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
364 | void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
519 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
583 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
260 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
337 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_bonded_cg_distance(const gmx::MDLogger&, const gmx_mtop_t*, const t_inputrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], gmx_bool, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1991:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1991 | void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
412 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function 'void dd_move_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void dd_move_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function 'void dd_clear_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:77:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | void dd_clear_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f)
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >; <template-parameter-2-2> = void; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type 'std::vector<t_iparams>::const_iterator' changed in GCC 7.1
1379 | insert(const_iterator __position, _InputIterator __first,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_make_local_top(gmx_domdec_t*, gmx_domdec_zones_t*, int, real (*)[3], real*, const int*, t_forcerec*, real (*)[3], const gmx_mtop_t&, gmx_localtop_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:99: note: parameter passing for argument of type 'std::vector<t_iparams>::const_iterator' changed in GCC 7.1
1028 | iparams_dest.insert(iparams_dest.end(), iparams_src.begin(), iparams_src.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:99: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/stl_vector.h: In function 'void check_assign_interactions_atom(int, int, int, int, int, gmx::ArrayRef<const int>, gmx::ArrayRef<const int>, gmx_bool, int, int, const gmx_domdec_t*, const gmx_domdec_zones_t*, const gmx_molblock_t*, gmx_bool, const int*, gmx_bool, real, t_pbc*, real (*)[3], const t_iparams*, InteractionDefinitions*, int, gmx_bool, int*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
254 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void checkNumberOfBondedInteractions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], bool*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3222:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3222 | void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3235:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3235 | dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3236 | top_local, x, box); // Does not return
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
70 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
80 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:109:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
109 | impl_->scale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
112 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:114:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
114 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:119:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
119 | impl_->inverseIgnoringZeroScale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
155 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:176:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
176 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:178:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
178 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:183:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
183 | impl_->transform({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In constructor 'gmx::AffineTransformation::AffineTransformation(gmx::Matrix3x3ConstSpan, const RVec&)':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:211:1: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
211 | AffineTransformation::AffineTransformation(Matrix3x3ConstSpan matrix, const RVec& translation) :
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::AffineTransformation::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:217:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
217 | void AffineTransformation::operator()(ArrayRef<RVec> vectors) const
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::AffineTransformation::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:228:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
228 | (*this)({ vector, vector + 1 });
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2105 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx::ForceBuffers*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx::VirtualSitesHandler*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2867:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2867 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2908:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2908 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2929:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2929 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2947 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2948 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2971 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2972 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2973 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3006:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3006 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3009 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function 'gmx::Matrix3x3 gmx::transpose(gmx::Matrix3x3ConstSpan)':
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:50:11: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
50 | Matrix3x3 transpose(Matrix3x3ConstSpan matrixView)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function 'void gmx::matrixVectorMultiply(gmx::Matrix3x3ConstSpan, gmx::RVec*)':
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:58:6: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
58 | void matrixVectorMultiply(Matrix3x3ConstSpan matrix, RVec* v)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/units.cpp.o -MF CMakeFiles/libgromacs.dir/math/units.cpp.o.d -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp: In function 'gmx::OptimisationResult gmx::nelderMead(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>, real, int)':
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp:51:20: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
51 | OptimisationResult nelderMead(const std::function<real(ArrayRef<const real>)>& functionToMinimize,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp: In constructor 'gmx::NelderMeadSimplex::NelderMeadSimplex(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
100 | NelderMeadSimplex::NelderMeadSimplex(const std::function<real(ArrayRef<const real>)>& f,
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::ForceBuffers::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::ForceBuffers::ForceBuffers(bool, gmx::PinningPolicy)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::ForceBuffers::ForceBuffers()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/multipletimestepping.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:270:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
270 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void printLambdaStateToLog(FILE*, gmx::ArrayRef<double>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:344:6: note: parameter passing for argument of type 'const gmx::ArrayRef<double>' changed in GCC 7.1
344 | void printLambdaStateToLog(FILE* fplog, const gmx::ArrayRef<real> lambda, const bool isInitialOutput)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:357:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
357 | void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:407:26: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
407 | printLambdaStateToLog(fplog, lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function 'void gmx::shiftAtoms(const RVec&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:124:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | void shiftAtoms(const RVec& shift, ArrayRef<RVec> x)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function 'void gmx::placeCoordinatesWithCOMInBox(const PbcType&, gmx::UnitCellType, gmx::CenteringType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_mtop_t&, gmx::COMShiftType)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | void placeCoordinatesWithCOMInBox(const PbcType& pbcType,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
86 | put_atoms_in_compact_unitcell(pbcType, static_cast<int>(centerType), box, comArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:163:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1399:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1399 | void put_atoms_in_box(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1459:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1459 | void put_atoms_in_box_omp(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1475:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1475 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(PbcType, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1532:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1532 | void put_atoms_in_compact_unitcell(PbcType pbcType, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1532:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, PbcType, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, PbcType, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
347 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/output.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/output.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.h:54,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
944 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
56 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
65 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
102 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
91 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
71 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
78 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
85 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
233 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
822 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
875 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
372 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
916 | dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
917 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2248 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
156 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/10/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
156 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:114:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
114 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int, const string&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function 'void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, PbcType, real (*)[3], const string&, const real*, RotationType)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:171:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:589:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
589 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | &x_, removableAtoms, atomsInserted, xInserted, pbcTypeForOutput, box_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
591 | positionFile_, deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
343 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'gmx::index' {aka 'int'} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'gmx::index' {aka 'int'} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void checkPullCoords(gmx::ArrayRef<const t_pull_group>, gmx::ArrayRef<const t_pull_coord>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:484:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_pull_coord>' changed in GCC 7.1
484 | void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups, gmx::ArrayRef<const t_pull_coord> pullCoords)
| ^~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/10/bits/vector.tcc:161:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:546:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
546 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
547 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
548 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:577:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
577 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
578 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = t_pull_coord; _Alloc = std::allocator<t_pull_coord>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_pull_coord>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<std::__cxx11::basic_string<char> > read_pullparams(std::vector<t_inpfile>*, pull_params_t*, warninp_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_pull_coord*, std::vector<t_pull_coord> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1335:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1335 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2399:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2399 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_, logger);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool, gmx::ArrayRef<const int>, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
808 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
822 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
823 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
824 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
829 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
749 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
95 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, const gmx::MDLogger&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
232 | InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
217 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
341 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2657 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
542 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1985 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite3out_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
544 | static bool calc_vsite3out_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2337 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2444 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2575 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
128 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
712 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
731 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
849 | bERROR = calc_vsite3out_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
136 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
852 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1020 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2607 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool, const gmx::MDLogger&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1246 | put_atoms_in_compact_unitcell(pbcType, ecenter, fr.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1247 | positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(MPI_Comm, bool, bool, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:52:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
52 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function '_ZN3gmx11Constraints4Impl5applyEbbxidNS_19ArrayRefWithPaddingINS_11BasicVectorIdEEEES5_NS_8ArrayRefIS4_EEPA3_KddPdS5_bPA3_dNS_18ConstraintVariableE._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
575 | settle_proj(*settled, econq, end_th - start_th,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
576 | settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
577 | pbc_null, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
578 | min_proj, calcvir_atom_end,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const ListOfLists<int>& at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'int gmx::countFlexibleConstraints(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:869:5: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
869 | int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function 'bool gmx::Constraints::Impl::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:363:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
363 | bool Constraints::Impl::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:464:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_move_x_constraints(cr->dd, box, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
465 | econq == ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
479 | bOK = constrain_lincs(bLog || bEner, ir, step, lincsd, inverseMasses_, cr, ms, x, xprime,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
480 | min_proj, box, pbc_null, hasMassPerturbedAtoms_, lambda, dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
481 | invdt, v.unpaddedArrayRef(), computeVirial, constraintsVirial, econq,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
482 | nrnb, maxwarn, &warncount_lincs);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
496 | bOK = constrain_shake(log, shaked.get(), inverseMasses_, *idef, ir, x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
497 | xprime.unpaddedArrayRef(), min_proj, pbc_null, nrnb, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
498 | dvdlambda, invdt, v.unpaddedArrayRef(), computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
499 | constraintsVirial, maxwarn < INT_MAX, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function 'bool gmx::Constraints::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:342:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
342 | bool Constraints::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:358:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
358 | return impl_->apply(bLog, bEner, step, delta_step, step_scaling, std::move(x),
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
359 | std::move(xprime), min_proj, box, lambda, dvdlambda, std::move(v),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | computeVirial, constraintsVirial, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'void gmx::constrain_velocities(gmx::Constraints*, bool, bool, int64_t, t_state*, real*, gmx_bool, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1277:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1277 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278 | state->v.arrayRefWithPadding(), state->v.arrayRefWithPadding().unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1279 | state->box, state->lambda[efptBONDED], dvdlambda, ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1280 | computeVirial, constraintsVirial, ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'void gmx::constrain_coordinates(gmx::Constraints*, bool, bool, int64_t, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real*, gmx_bool, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1296:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1296 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(), std::move(xp),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1297 | ArrayRef<RVec>(), state->box, state->lambda[efptBONDED], dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1298 | state->v.arrayRefWithPadding(), computeVirial, constraintsVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1299 | ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'gmx::ListOfLists<int> gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:860:18: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
860 | ListOfLists<int> make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'gmx::ListOfLists<int> gmx::make_at2con(int, gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:852:18: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
852 | ListOfLists<int> make_at2con(int numAtoms,
| ^~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::do_constrain_first(FILE*, gmx::Constraints*, const t_inputrec*, int, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1218:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1218 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, x, {}, box, lambda, &dvdl_dum, {},
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1219 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1224:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1224 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, v, v.unpaddedArrayRef(), box, lambda,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1225 | &dvdl_dum, {}, computeVirial, nullptr, gmx::ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1251:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1251 | constr->apply(needsLogging, computeEnergy, step, -1, 1.0, x, savex.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1252 | {}, box, lambda, &dvdl_dum, v, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1253 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1268 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:293:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
321 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->getAndersenRandomizeGroup(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
322 | upd->getBoltzmanFactor());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:108:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
108 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:199:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
199 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::BoxDeformation*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:289:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | boxDeformation->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:518:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
518 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:528:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
528 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:219:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
219 | void accumulatePotentialEnergies(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda* fepvals)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const double>, double, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
245 | void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const real> energyTerms,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulateKineticLambdaComponents(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:280:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
280 | void accumulateKineticLambdaComponents(gmx_enerdata_t* enerd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
296 | enerd->foreignLambdaTerms.finalizeKineticContributions(enerd->term, enerd->dvdl_lin[efptMASS],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | lambda, fepvals);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void calculateLongRangeNonbondeds(t_forcerec*, const t_inputrec*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, gmx_enerdata_t*, const real (*)[3], const real*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
101 | void calculateLongRangeNonbondeds(t_forcerec* fr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
197 | status = gmx_pme_do(
| ~~~~~~~~~~^
198 | fr->pmedata,
| ~~~~~~~~~~~~
199 | gmx::constArrayRefFromArray(coordinates.data(), md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | forceWithVirial->force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
206 | &ewaldOutput.dvdl[efptVDW], stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
226 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
227 | fr->pmedata, coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/freeenergyparameters.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_lambda*, const t_expanded*, const real (*)[3], gmx::PTCouplingArrays, int, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:891:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
891 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:49:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, real)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void compute_globals(gmx_global_stat*, t_commrec*, const t_inputrec*, t_forcerec*, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_mdatoms*, t_nrnb*, t_vcm*, gmx_wallcycle_t, gmx_enerdata_t*, real (*)[3], real (*)[3], real (*)[3], real (*)[3], gmx::Constraints*, gmx::SimulationSignaller*, const real (*)[3], int*, gmx_bool*, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
297 | void compute_globals(gmx_global_stat* gstat,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
366 | calc_vcm_grp(*mdatoms, x, v, vcm);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
712 | as_rvec_array(fp.data()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1086:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1086 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1107:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1107 | dd_move_x_constraints(cr->dd, box, xpPadded.unpaddedArrayRef(), ArrayRef<RVec>(), FALSE);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1155:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1155 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'bool gmx::constrain_lincs(bool, const t_inputrec&, int64_t, gmx::Lincs*, const real*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], t_pbc*, bool, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable, t_nrnb*, int, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2259 | bool constrain_lincs(bool computeRmsd,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resizeChargeA(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resizeChargeB(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::set_lincs(const InteractionDefinitions&, int, const real*, real, bool, const t_commrec*, gmx::Lincs*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1911:94: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
1911 | make_at2con(natoms, idef.il, idef.iparams, flexibleConstraintTreatment(bDynamics));
| ^
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::WriteCheckpointDataHolder*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:513:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
513 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | state_local->cg_gl, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
546 | state_local->cg_gl, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
552 | dd_collect_vec(
| ~~~~~~~~~~~~~~^
553 | cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp: In function 'void gmx::settle_proj(const gmx::SettleData&, gmx::ConstraintVariable, int, const t_iatom*, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
260 | void settle_proj(const SettleData& settled,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'void gmx::cshake(const int*, int, int*, int, gmx::ArrayRef<const double>, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
270 | void cshake(const int iatom[],
| ^~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'bool gmx::bshakef(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
655 | static bool bshakef(FILE* log,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
505 | cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime, pbc, rij,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
506 | half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
507 | scaled_lagrange_multiplier, &error);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'bool gmx::constrain_shake(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
761 | bool constrain_shake(FILE* log,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
788 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
789 | invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
792 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, vprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
793 | invdt, {}, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void postProcessForceWithShiftForces(t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms&, const t_forcerec&, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:282:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
282 | static void postProcessForceWithShiftForces(t_nrnb* nrnb,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
307 | vsite->spreadForces(x, f, virialHandling, fshift, nullptr, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void postProcessForces(const t_commrec*, int64_t, t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms*, const t_forcerec*, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:320:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
320 | static void postProcessForces(const t_commrec* cr,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
357 | vsite->spreadForces(x, forceWithVirial.force_, virialHandling, {}, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const double>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1125:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1125 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1236:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1236 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1279:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1279 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1306:62: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1306 | fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1325:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1325 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1326 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1332:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1332 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1336 | nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1337 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr), fr->cginfo);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1487:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1487 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1505:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1505 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1513 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1674:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1674 | nbv->dispatchFreeEnergyKernel(InteractionLocality::Local, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1675 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1676 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1677 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1681:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1681 | nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1682 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1683 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1684 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1713:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1713 | nbnxn_atomdata_add_nbat_fshift_to_fshift(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
1714 | *nbv->nbat, forceOutNonbonded->forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1732:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1732 | real dvdl_walls = do_walls(*inputrec, *fr, box, *mdatoms, x.unpaddedConstArrayRef(),
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | &forceOutMtsLevel0.forceWithVirial(), lambda[efptVDW],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | enerd->grpp.ener[egLJSR].data(), nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1764:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1764 | listedForces.calculate(
| ~~~~~~~~~~~~~~~~~~~~~~^
1765 | wcycle, box, inputrec->fepvals, cr, ms, x, xWholeMolecules, fr->fcdata.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1766 | hist, &forceOut, fr, &pbc, enerd, nrnb, lambda.data(), mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1767 | DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1773:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1773 | calculateLongRangeNonbondeds(fr, inputrec, cr, nrnb, wcycle, mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1774 | x.unpaddedConstArrayRef(), &forceOutMtsLevel1->forceWithVirial(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1775 | enerd, box, lambda.data(), as_rvec_array(dipoleData.muStateAB),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1776 | stepWork, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1845:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1845 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1846 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1855:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1855 | stateGpu->copyForcesFromGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1856 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1866:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1866 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1901:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1901 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1902 | AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2032:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2032 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2049:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2049 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2077 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2078 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2105:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2105 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2106 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2116:36: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2116 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
58 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:149:41: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
149 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | state_global, observablesHistory, f, &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function 'void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In member function 'void gmx::Update::Impl::update_sd_second_half(const t_inputrec&, int64_t, real*, const t_mdatoms*, t_state*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, gmx::Constraints*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1403:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1403 | constr->apply(do_log, do_ene, step, 1, 0.5, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1404 | xp_.arrayRefWithPadding(), ArrayRef<RVec>(), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | state->lambda[efptBONDED], dvdlambda, state->v.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | computeVirial, nullptr, ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:340:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
340 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:359:85: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
359 | FlexibleConstraintTreatment::Include);
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function 'void calc_vcm_grp(const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_vcm*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
155 | void calc_vcm_grp(const t_mdatoms& md,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function 'void process_and_stopcm_grp(FILE*, t_vcm*, const t_mdatoms&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
579 | void process_and_stopcm_grp(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec&, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp: In function 'real do_walls(const t_inputrec&, const t_forcerec&, const real (*)[3], const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, real, real*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp:162:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
162 | real do_walls(const t_inputrec& ir,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function 'void gmx::WholeMoleculeTransform::updateForAtomPbcJumps(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function 'gmx::ArrayRef<const gmx::BasicVector<double> > gmx::WholeMoleculeTransform::wholeMoleculeCoordinates(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:62:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
62 | ArrayRef<const RVec> WholeMoleculeTransform::wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::construct_vsites_thread(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
625 | static void construct_vsites_thread(ArrayRef<RVec> x,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::construct_vsites(const gmx::ThreadingInfo*, gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const gmx::DomainInfo&, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
769 | static void construct_vsites(const ThreadingInfo* threadingInfo,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:809:32: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
809 | construct_vsites_thread(x, dt, v, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:835:32: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
835 | construct_vsites_thread(x, dt, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function '_ZN3gmxL16construct_vsitesEPKNS_13ThreadingInfoENS_8ArrayRefINS_11BasicVectorIdEEEEdS6_NS3_IK9t_iparamsEENS3_IK15InteractionListEERKNS_10DomainInfoEPA3_Kd._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:822:40: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
822 | construct_vsites_thread(x, dt, v, ip, tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:829:44: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
829 | construct_vsites_thread(x, dt, v, ip, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::spreadForceForThread(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*) [with gmx::VirtualSitesHandler::VirialHandling virialHandling = gmx::VirtualSitesHandler::VirialHandling::NonLinear]':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1728 | static void spreadForceForThread(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::spreadForceWrapper(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], bool, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1823 | static void spreadForceWrapper(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1847 | spreadForceForThread<VirialHandling::NonLinear>(x, f, fshift, dxdf, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function '_ZN3gmx19VirtualSitesHandler4Impl12spreadForcesENS_8ArrayRefIKNS_11BasicVectorIdEEEENS2_IS4_EENS0_14VirialHandlingES7_PA3_dP6t_nrnbPA3_KdP13gmx_wallcycle._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2006 | spreadForceWrapper(x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2007 | tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1969 | spreadForceWrapper(x, idTask->force, virialHandling, fshift_t, tData.dxdf, true,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1970 | iparams_, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
839 | void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
841 | construct_vsites(&threadingInfo_, x, dt, v, iparams_, ilists_, domainInfo_, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
844 | void VirtualSitesHandler::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
846 | impl_->construct(x, dt, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::constructVirtualSites(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
849 | void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
854 | construct_vsites(nullptr, x, 0, {}, ip, ilist, domainInfo, nullptr);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::constructVirtualSitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:917:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
917 | void constructVirtualSitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1868 | void VirtualSitesHandler::Impl::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1898:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1898 | dd_clear_f_vsites(*domainInfo_.domdec_, f);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1906 | spreadForceWrapper(x, f, virialHandling, fshift, dxdf, true, iparams_, ilists_, pbc_null);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1923 | spreadForceWrapper(x, f, virialHandling, fshift, nlDependentVSites.dxdf, true, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1924 | nlDependentVSites.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2043 | dd_move_f_vsites(*domainInfo_.domdec_, f, fshift);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2097 | void VirtualSitesHandler::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2106 | impl_->spreadForces(x, f, virialHandling, fshift, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::ThreadingInfo::setVirtualSites(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, const t_mdatoms&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2434:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
2434 | void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::setVirtualSites(gmx::ArrayRef<const InteractionList>, const t_mdatoms&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2698:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
2698 | threadingInfo_.setVirtualSites(ilists, iparams_, mdatoms, domainInfo_.useDomdec());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2698:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function 'real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN3gmx13ThreadingInfo15setVirtualSitesENS_8ArrayRefIK15InteractionListEENS1_IK9t_iparamsEERK9t_mdatomsb._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]':
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1921 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1353:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1353 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1407:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1407 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:276:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
276 | (*affineTransformation_)(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:292:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
292 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:340:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
340 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
In file included from /usr/include/c++/10/bits/node_handle.h:39,
from /usr/include/c++/10/bits/hashtable.h:37,
from /usr/include/c++/10/unordered_map:46,
from /usr/include/c++/10/functional:61,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:44:
/usr/include/c++/10/optional: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, PbcType, double, const gmx::DensityFittingForceProviderState&)':
/usr/include/c++/10/optional:418:4: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >' changed in GCC 7.1
418 | ::new
| ^~~~~
419 | (std::__addressof(static_cast<_Dp*>(this)->_M_payload._M_payload))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
420 | _Stored_type(std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp: In member function 'void ListedForces::calculate(gmx_wallcycle*, const real (*)[3], const t_lambda*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_fcdata*, history_t*, gmx::ForceOutputs*, const t_forcerec*, const t_pbc*, gmx_enerdata_t*, t_nrnb*, const real*, const t_mdatoms*, int*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
698 | void ListedForces::calculate(struct gmx_wallcycle* wcycle,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:760:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
760 | enerd->term[F_ORIRESDEV] = calc_orires_dev(
| ~~~~~~~~~~~~~~~^
761 | ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(), idef.iparams.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
762 | md, xWholeMolecules, x, fr->bMolPBC ? pbc : nullptr, fcdata->orires, hist);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp: In function 'real calc_orires_dev(const gmx_multisim_t*, int, const t_iatom*, const t_iparams*, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_pbc*, t_oriresdata*, history_t*)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp:384:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
384 | real calc_orires_dev(const gmx_multisim_t* ms,
| ^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:555:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
555 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:901:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
901 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1040:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1040 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:960:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
960 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:960:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode, const gmx::DeviceStreamManager*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:720:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
720 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
737 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
738 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
739 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
740 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
741 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | &dvdlambda_lj, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1012:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1012 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1012:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1161:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1161:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1378:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1378 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1378:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1387:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1387 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1387:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/prepare_detection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
300 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
301 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
302 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:305:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
305 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
306 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
307 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
392 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:424:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
424 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
427 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
428 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
429 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:440:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
440 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:453:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
455 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
456 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
468 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
469 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
470 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
471 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
472 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
473 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:475:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
475 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
476 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
487 | dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
488 | flocal, ftemp);
| ~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:512:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
512 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:51:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:257:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
257 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
515 | vsite->construct(state->x, ir->delta_t, {}, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
586 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
587 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
588 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
589 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | cglo_flags_iteration
| ~~~~~~~~~~~~~~~~~~~~
591 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
600 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:604:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
604 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
605 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
615 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
616 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
617 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
618 | state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:737:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
737 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:741:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
741 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
743 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:798:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
798 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:803:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
803 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
865 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
866 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
867 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
868 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
869 | CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:870:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
870 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
871 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
872 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1007 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1008 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1009 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1010 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1011 | (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1012 | | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1013 | | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1014 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1015 | : 0)
| ~~~~
1016 | | CGLO_SCALEEKIN);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1024:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1024 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1025 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1026 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1029 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1030 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1068 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1069 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1070 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1071 | state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1099:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1099 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1127:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1127 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1135:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1135 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1151:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1151 | stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1158:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1158 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1159 | observablesHistory, top_global, fr, outf, energyOutput, ekind,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | f.view().force(), checkpointHandler->isCheckpointingStep(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1193:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1193 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1268:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1268 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1269:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1269 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1276:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1276 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1282:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1282 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1299:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1299 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1346 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1347 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1348 | nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1391 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1410:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1410 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1423 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1424 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1425 | wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1426 | &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1427 | (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1428 | | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1429 | | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1430 | | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1431 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1432 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1433:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1433 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1434 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1435 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1438 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1439 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1445:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1445 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1453:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1453 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1471:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1471 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1572:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1572 | printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
834 | vsite->construct(ems->s.x, 1, {}, ems->s.box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:848:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
848 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, &ems->f.view(), force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | mdAtoms->mdatoms(), enerd, ems->s.lambda, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
852 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
853 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:896:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
896 | constr->apply(needsLogging, computeEnergy, count, 0, 1.0, ems->s.x.arrayRefWithPadding(), f,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | f.unpaddedArrayRef(), ems->s.box, ems->s.lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
898 | gmx::ArrayRefWithPadding<RVec>(), computeVirial, shake_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
899 | gmx::ConstraintVariable::ForceDispl);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:913:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
913 | accumulateKineticLambdaComponents(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, const gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, gmx::MDAtoms*, gmx_global_stat**, gmx::VirtualSitesHandler*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:397:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
397 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:461:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
461 | constr->apply(needsLogging, computeEnergy, -1, 0, 1.0, ems->s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | ems->s.x.arrayRefWithPadding(), ArrayRef<RVec>(), ems->s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
463 | ems->s.lambda[efptFEP], &dvdl_constr, gmx::ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | dd_collect_vec(cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | state->s.x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1765 | vsite->construct(state_global->x, 1, {}, state_global->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1867:41: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1867 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1868 | static_cast<real>(step), &ems.s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1869 | ems.f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:285:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
285 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
354 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
355 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
356 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
357 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:359:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
359 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
361 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
165 | vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:540:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
540 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
542 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
544 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
545 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:556:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
556 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
557 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
558 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
559 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:569:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
569 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
572 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
580 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
593 | enerd, force_vir, shake_vir, total_vir, pres, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
594 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
595 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
596 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
597 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:598:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
598 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
599 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
600 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2774:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2774 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2775 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2776 | state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2777 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2778 | state_work.s.lambda, &state_work.s.hist, &state_work.f.view(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2779 | vir, mdatoms, nrnb, wcycle, shellfc, fr, runScheduleWork, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2780 | mu_tot, vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, em_state_t*, gmx::Constraints*, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:689:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
689 | validStep = constr->apply(
| ~~~~~~~~~~~~~^
690 | TRUE, TRUE, count, 0, 1.0, s1->x.arrayRefWithPadding(), s2->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
691 | ArrayRef<RVec>(), s2->box, s2->lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
692 | gmx::ArrayRefWithPadding<RVec>(), false, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void pr_shell(FILE*, gmx::ArrayRef<const t_shell>)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:126:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
126 | static void pr_shell(FILE* fplog, ArrayRef<const t_shell> shells)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'real rms_force(const t_commrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const t_shell>, int, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:778:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
778 | static real rms_force(const t_commrec* cr,
| ^~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_shell&}; _Tp = t_shell; _Alloc = std::allocator<t_shell>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_shell>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::make_local_shells(const t_commrec*, const t_mdatoms*, gmx_shellfc_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_shell*, std::vector<t_shell> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void init_adir(gmx_shellfc_t*, gmx::Constraints*, const t_inputrec*, const t_commrec*, int, int64_t, const t_mdatoms*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:828:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
828 | static void init_adir(gmx_shellfc_t* shfc,
| ^~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:890:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
890 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
891 | shfc->adir_xnold.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
892 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
893 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:894:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
894 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
895 | shfc->adir_xnew.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
896 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:910:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
910 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xOld, shfc->adir_xnew.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
911 | acc_dir, box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
912 | nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'gmx_shellfc_t* init_shell_flexcon(FILE*, const gmx_mtop_t*, int, int, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:427:41: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
427 | pr_shell(fplog, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:498:17: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
498 | pr_shell(debug, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, gmx::VirtualSitesHandler*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:915:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
915 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1039:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1039 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1040 | nrnb, wcycle, top, box, xPadded, hist, &forceViewInit, force_vir, md, enerd, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1042 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1055:32: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1055 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1047:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1047 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old.arrayRefWithPadding(),
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1048 | x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1104 | vsite->construct(pos[Min], inputrec->delta_t, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1109:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1109 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1110 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1111 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1126:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1126 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1127 | top, box, posWithPadding[Try], hist, &forceViewTry, force_vir, md, enerd, lambda, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1128 | runScheduleWork, vsite, mu_tot, t, nullptr, shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1129:36: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1129 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1138:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1138 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1139 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1140 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp: In member function 'void gmx::LegacySimulator::do_tpi()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:605:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
605 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:677:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
677 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
678 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
681 | fr->nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
682 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
683 | fr->cginfo);
| ~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
738 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:756:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
756 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
757 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
758 | &state_global->hist, &f.view(), force_vir, mdatoms, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
759 | state_global->lambda, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
760 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
761 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | putUpdateGroupAtomsInSamePeriodicImage(*cr->dd, mtop, globalState->box, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1526:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1526 | constructVirtualSitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:129:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
129 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:144:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
144 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:161:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
161 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:177:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
177 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:201:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
226 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -MF CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/options.cpp.o -MF CMakeFiles/libgromacs.dir/options/options.cpp.o.d -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -MF CMakeFiles/libgromacs.dir/options/treesupport.cpp.o.d -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In static member function 'static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:830:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
830 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o 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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.6.0.0 ../../lib/libgromacs_d.so.6 ../../lib/libgromacs_d.so
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.6.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxsetup.cpp.o -MF CMakeFiles/nblib.dir/gmxsetup.cpp.o.d -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/integrator.cpp
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function 'void nblib::ForceCalculator::updatePairList(gmx::ArrayRef<const int>, gmx::ArrayRef<gmx::BasicVector<double> >, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
73 | void ForceCalculator::updatePairList(gmx::ArrayRef<const int> particleInfoAllVdW,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
77 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdW, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function 'void nblib::ForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
63 | void ForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
70 | gmxForceCalculator_->compute(coordinates, forces);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/interactions.cpp
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp: In member function 'void nblib::LeapFrog::integrate(real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
63 | void LeapFrog::integrate(const real dt, gmx::ArrayRef<Vec3> x, gmx::ArrayRef<Vec3> v, gmx::ArrayRef<const Vec3> f)
| ^~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function 'void nblib::GmxForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
70 | void GmxForceCalculator::compute(gmx::ArrayRef<const gmx::RVec> coordinateInput,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
74 | nbv_->convertCoordinates(gmx::AtomLocality::Local, false, coordinateInput);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function 'void nblib::GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
82 | void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int> particleInfoAllVdw,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:97:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
97 | nbnxn_put_on_grid(nbv_.get(), legacyBox, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
98 | { 0, int(coordinates.size()) }, particleDensity, particleInfoAllVdw,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
99 | coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particlesequencer.cpp
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setAtomProperties(const std::vector<int>&, const std::vector<double>&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
172 | gmxForceCalculator_->nbv_->setAtomProperties(particleTypeIdOfAllParticles, charges, particleInfoAllVdw_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setParticlesOnGrid(const std::vector<gmx::BasicVector<double> >&, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
298 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdw_, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setupNbnxmInstance(size_t, const nblib::NBKernelOptions&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:199:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
199 | nbnxn_atomdata_init(gmx::MDLogger(), atomData.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | numParticleTypes, nonbondedParameters_, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/api/nblib/vector.h:47,
from /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.h:52,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.h:51,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void nblib::NbvSetupUtil::setNonBondedParameters(const std::vector<nblib::ParticleType>&, const nblib::NonBondedInteractionMap&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/simulationstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topologyhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topology.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::ParticleData}; _Tp = nblib::ParticleData; _Alloc = std::allocator<nblib::ParticleData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {0}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {1}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {2}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {3}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {4}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const FiveCenterInteraction&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {1}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {2}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {0}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const ThreeCenterInteraction&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'nblib::Molecule& nblib::Molecule::addParticle(const ParticleName&, const ResidueName&, const Charge&, const nblib::ParticleType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleData*, std::vector<nblib::ParticleData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/transformations.cpp
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
85 | void ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const Vec3> x, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
151 | computeForcesAndEnergies(coordinates, usePbc);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, nblib::ListedForceCalculator::EnergyType&, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
159 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | compute(coordinates, forces, usePbc);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/setup.cpp
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2053 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function 'bool nblib::isRealValued(gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:124:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
124 | bool isRealValued(gmx::ArrayRef<const Vec3> values)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function 'void nblib::zeroCartesianArray(gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:139:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
139 | void zeroCartesianArray(gmx::ArrayRef<Vec3> cartesianArray)
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::CubicBondType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::HarmonicAngleType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ImproperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::Default5Center, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::CubicBondType]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::Default5Center]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::RyckaertBellemanDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ImproperDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::HarmonicAngleType]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ProperDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::CubicBondType]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::HarmonicAngleType]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ProperDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2169:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2169 | = std::__upper_bound(++__middle, __first, __val, __comp_val_it);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h:2133:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2133 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2134 | __gnu_cxx::__ops::__val_comp_iter(__comp));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ImproperDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::RyckaertBellemanDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::Default5Center]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'nblib::Topology nblib::TopologyBuilder::buildTopology()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp: In function 'int main()':
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:89:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
89 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:96:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
96 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:103:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
103 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
120 | forceCalculator.compute(simState.coordinates(), userForces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp: In function 'int main()':
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:157:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
157 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:172:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
172 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | forceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
203 | listedForceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | integrator.integrate(1.0, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
207 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
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/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulatorcomparison.cpp
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/usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o
/usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nullptr, step, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target applied_forces-test
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
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[ 70%] Built target onlinehelp-test-shared
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target domdec-mpi-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -MF CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o.d -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mutex.cpp.o -MF CMakeFiles/utility-test.dir/mutex.cpp.o.d -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_buffer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/typecasts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target mdtypes-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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[ 76%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/listoflists.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/range.cpp.o CMakeFiles/utility-test.dir/strconvert.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/template_mp.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target utility-test
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target options-test
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target table-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target math-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
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[ 87%] Built target analysisdata-test-shared
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target coordinateio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function 'static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-tpi-test
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target nblib-setup-test
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-integration-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-util-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib /<<PKGBUILDDIR>>/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
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make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'.
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[ 98%] Built target nblib-tests
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (0 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (0 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms)
1: [----------] 5 tests from NBlibTest (0 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (0 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (1 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms)
1: [----------] 5 tests from ListedExampleData (2 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (4 ms)
1: [----------] 1 test from LinearChainDataFixture (4 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (0 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (0 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (1 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (1 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (1 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (1 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (10 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 0.04 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.02 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.132611 y 4.369854 z 5.148869
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.03 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (0 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (2 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms)
4: [----------] 10 tests from NblibTraitsUtils (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (4 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.03 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (1 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (1 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (0 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (0 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (1 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (1 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (1 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (1 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (11 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (11 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.04 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (2 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (1 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (1 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (2 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (1 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (0 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms)
6: [----------] 19 tests from NBlibTest (13 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (13 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.04 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (1 ms)
7: [----------] 1 test from NBlibTest (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (1 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.03 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (17 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (28 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (2 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (1 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (1 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (2 ms)
8: [----------] 4 tests from XvgTests (6 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (52 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.08 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (1 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.02 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (2 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (0 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (2 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (2 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (2 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
10: [----------] 2 tests from CStringUtilityTest (0 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (1 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (1 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
10: [----------] 6 tests from TreeValueTransformTest (2 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (0 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (0 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (1 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (1 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (1 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (0 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (2 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
10: [----------] 7 tests from LoggerTest (5 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (0 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (1 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (1 ms)
10: [----------] 2 tests from PathTest (1 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (1 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (0 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (1 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (2 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (3 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (0 ms)
10: [----------] 1 test from JoinStringsTest (0 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (1 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
10: [----------] 10 tests from TextLineWrapperTest (2 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (1 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (1 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
10: [----------] 6 tests from TextWriterTest (2 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (1 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (4 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (58 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.12 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (3 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (4 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.03 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
12: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (1 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms)
12: [----------] 2 tests from PrEbinTest (2 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (0 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (1 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (0 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (2 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (0 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (0 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (1 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (0 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (2 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms)
12: [----------] 1 test from UpdateGroupsCog (3 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (1 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (6 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (8 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (41 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (13 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (184 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (5 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (1 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (2 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (6 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (19 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (7 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (104 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (4 ms)
12: [----------] 13 tests from WithParameters/SettleTest (36 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (355 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 0.44 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (1 ms)
13: [----------] 1 test from BiasTest (1 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (3 ms)
13: [----------] 1 test from biasGridTest (3 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (6 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (6 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms)
13: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (2 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (13 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (12 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (13 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (12 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (54 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (73 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.10 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (1 ms)
14: [----------] 2 tests from DensityFittingTest (2 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms)
14: [----------] 1 test from DensityFittingForceProviderState (0 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (5 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.03 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (1 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (0 ms)
15: [----------] 3 tests from ElectricFieldTest (1 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (1 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.02 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (1 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (11 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (15 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (9 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (4 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (9 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (50 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.10 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (4 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
17: [----------] 13 tests from CommandLineParserTest (2 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
17: [----------] 3 tests from OutputNamesTest (0 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (2 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
17: [----------] 21 tests from ParseCommonArgsTest (7 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (22 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.05 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (0 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (1 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
18: [----------] 2 tests from LocalAtomSetManager (1 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (1 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.03 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (3 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (4 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (8 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (4 ms)
19: [----------] 4 tests from HaloExchangeTest (19 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (20 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.07 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (6 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (5 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (118 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (70 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (49 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (16 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (30 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (46 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (56 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (72 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (9 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (14 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (16 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (20 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (23 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (10 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (14 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (15 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (19 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (21 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (222 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (686 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 0.79 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (9 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (14 ms)
21: [----------] 2 tests from ManyFFTTest (24 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (6 ms)
21: [----------] 1 test from FFTTest (6 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
21: [----------] 1 test from FFFTest3D (3 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (8 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (12 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (33 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (67 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.09 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (0 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (1 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (0 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (6 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.06 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (0 ms)
23: [----------] 1 test from CpuInfoTest (2 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: [ OK ] HardwareTopologyTest.Execute (19 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: [ OK ] HardwareTopologyTest.HwlocExecute (18 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (19 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (18 ms)
23: [----------] 4 tests from HardwareTopologyTest (76 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (79 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.10 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (2 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (0 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (1 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (60 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (61 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (154 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
24: [----------] 12 tests from DensitySimilarityTest (278 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (0 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (1 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (0 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (0 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (1 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (1 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
24: [----------] 21 tests from FunctionTest (6 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (0 ms)
24: [----------] 9 tests from GaussTransformTest (1 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (1 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (1 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (0 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (0 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (1 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (1 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (1 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (1 ms)
24: [----------] 2 tests from NelderMead (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (1 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (1 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (0 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (301 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.34 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (4 ms)
25: [----------] 17 tests from ThreadAffinityTest (19 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (20 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.04 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (13 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (10 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (8 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (11 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (51 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (13 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (7 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (8 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (6 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (26 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (8 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (6 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (75 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (128 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.15 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
27: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (0 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (1 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (0 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (0 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (1 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (1 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (1 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (4 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.03 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (7 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (50 ms)
28: [----------] 2 tests from CheckpointDataTest (57 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (0 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (58 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.08 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
29: [----------] 6 tests from TextTableFormatterTest (3 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
29: [----------] 3 tests from HelpManagerTest (2 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
29: [----------] 11 tests from HelpWriterContextTest (5 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (11 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.03 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (1 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (2 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (1 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
30: [----------] 1 test from OptionsTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (1 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (3 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (1 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (1 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (2 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (1 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
30: [----------] 7 tests from TreeValueSupportTest (3 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (26 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.05 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (0 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (1 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms)
31: [----------] 2 tests from MShift (1 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
31: [----------] 1 test from PbcTest (1 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (0 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (15 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (17 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.04 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (1 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (0 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (0 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (1 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (0 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (0 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (0 ms)
32: [----------] 1 test from SeedTest (0 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (0 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
32: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (0 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (0 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (0 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (10 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.05 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (0 ms)
33: [----------] 1 test from RestraintManager (0 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (1 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.02 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (2 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (26 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (2 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (3 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (51 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (58 ms)
34: [----------] 8 tests from SplineTableTest/0 (145 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (1 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (3 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (8 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (9 ms)
34: [----------] 8 tests from SplineTableTest/1 (31 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (177 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 0.20 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (3 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.02 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (1 ms)
36: [----------] 3 tests from ExclusionBlockTest (1 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (1 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (0 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (1 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (0 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (0 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (0 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms)
36: [----------] 13 tests from StringTableTest (6 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms)
36: [----------] 6 tests from LegacySymtabTest (1 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (11 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.03 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (1 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.02 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (0 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (0 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (6 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (1 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (0 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (5 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (12 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.04 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (0 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (1 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (0 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (1 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.02 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
40: [----------] 5 tests from Entropy (1 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (2 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (3 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (2 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (2 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (3 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (3 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (2 ms)
40: [----------] 10 tests from MindistTest (27 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (4 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
40: [----------] 3 tests from MsdTest (10 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -207368265
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (844 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -621413889
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (848 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to 1139793660
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (845 ms)
40: [----------] 3 tests from MsdMolTest (2538 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (26 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (2604 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 2.63 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 69 tests from 10 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (3 ms)
41: [----------] 4 tests from GenconfTest (8 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to -2113537
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (870 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to -583163905
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (856 ms)
41: [----------] 2 tests from GenionTest (1726 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (5 ms)
41: [----------] 1 test from GenRestrTest (5 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (5 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (4 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (20 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (4 ms)
41: [----------] 5 tests from InsertMoleculesTest (38 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (9 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (8 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (8 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (8 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (7 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (6 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (4 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (9 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (6 ms)
41: [----------] 14 tests from GetIrTest (106 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (20 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (101 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (102 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (48 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (403 ms)
41: [----------] 5 tests from SolvateTest (674 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (0 ms total)
41:
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (16 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (7 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (7 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (9 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (7 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (12 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (12 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (6 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (5 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (5 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (6 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (6 ms)
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest (165 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 69 tests from 10 test cases ran. (2725 ms total)
41: [ PASSED ] 69 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 2.75 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (181 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (201 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (182 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (165 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (194 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (211 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (199 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (179 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (177 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (197 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (181 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (164 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (191 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (210 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (197 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (178 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (178 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (198 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (182 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (166 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (192 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (210 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (197 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (178 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4509 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (4509 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 4.53 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (130 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (146 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (131 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (124 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (133 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (152 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (139 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (131 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (132 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (150 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (134 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (125 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (136 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (156 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (140 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (131 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2192 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (145 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (164 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (143 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (135 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (148 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (165 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (148 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (142 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (143 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (163 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (146 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (137 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (149 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (170 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (150 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (144 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2394 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (4586 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 4.61 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (177 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (196 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (178 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (161 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (190 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (213 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (200 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (178 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1494 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (66 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (66 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (167 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (188 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (176 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (156 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (182 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (202 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (189 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (170 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1433 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (172 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (126 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (169 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (127 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (173 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (129 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (167 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (130 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (1193 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (86 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (87 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (87 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (86 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (346 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (11425 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (826 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (34882 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (828 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (47961 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (52493 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 52.52 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (24 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (17 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (32 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (49 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (4 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (49 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (49 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (97 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (9 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (51 ms)
45: [----------] 10 tests from AutocorrTest (390 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (1 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (3 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (4 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (13 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (10 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (69 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (8 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (8 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (15 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (39 ms)
45: [----------] 10 tests from ExpfitTest (172 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
45: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (596 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 0.62 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (1 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (24 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (29 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (3 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (35 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (34 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (4 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
46: [----------] 6 tests from AverageModuleTest (28 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
46: [----------] 2 tests from FrameAverageModuleTest (9 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (13 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (20 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (5 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 3 tests from BinAverageModuleTest (16 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (10 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (29 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (3 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (4 ms)
46: [----------] 3 tests from LifetimeModuleTest (13 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (257 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.28 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (13 ms)
47: [----------] 1 test from OutputSelectorDeathTest (13 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (18 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (46 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (0 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (1 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (1 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (9 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (9 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (9 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (8 ms)
47: [----------] 5 tests from SetAtomsTest (44 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (1 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (1 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (0 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (0 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (9 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (9 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (9 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (52 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (9 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (8 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (25 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (19 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (18 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (73 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (9 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (9 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (26 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (9 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (1 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (9 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (8 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (9 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (35 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (353 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 0.38 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 85 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (11 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (11 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (11 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (14 ms)
48: [----------] 11 tests from AngleModuleTest (133 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (13 ms)
48: [----------] 5 tests from ClustsizeTest (48 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (19 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (103 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (104 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (12 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (229 ms total)
48:
48: [----------] 6 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (14 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (18 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: Contacts:
48: Number of samples: 2
48: Average distance: 1.00000 nm
48: Standard deviation: 0.00000 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (39 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: SuccessiveContacts:
48: Number of samples: 2
48: Average distance: 1.00000 nm
48: Standard deviation: 0.00000 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (39 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: ManyContacts:
48: Number of samples: 10
48: Average distance: 1.82913 nm
48: Standard deviation: 0.78478 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (40 ms)
48: [----------] 6 tests from DistanceModuleTest (169 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (12 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (13 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (25 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (764 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (765 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (1530 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (8 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (8 ms)
48: [----------] 9 tests from PairDistanceModuleTest (85 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (61 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (45 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (62 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (46 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (71 ms)
48: [----------] 5 tests from RdfModuleTest (286 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (35 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (22 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (19 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (29 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (29 ms)
48: [----------] 5 tests from SasaModuleTest (136 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (20 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (14 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (15 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (15 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (12 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
48: [----------] 8 tests from SelectModuleTest (108 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (10 ms)
48: [----------] 10 tests from SurfaceAreaTest (31 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (1 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (9 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
48: Setting the LD random seed to -713228297
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (970 ms)
48: [----------] 4 tests from TopologyInformation (988 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (12 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (11 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (10 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
48: [----------] 4 tests from TrajectoryModuleTest (43 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (1 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
48: [----------] 5 tests from UnionFinderTest (1 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
48: [----------] 1 test from MappedUnionFinderTest (0 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 85 tests from 16 test cases ran. (3832 ms total)
48: [ PASSED ] 85 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 3.86 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (123 ms)
49: [----------] 1 test from DhdlTest (125 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (261 ms)
49: [----------] 1 test from OriresTest (261 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (29 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (29 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (29 ms)
49: [----------] 3 tests from EnergyTest (89 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (63 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (57 ms)
49: [----------] 2 tests from ViscosityTest (122 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (597 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.62 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -1346817
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = -1346817
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 59458
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
50: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
50: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
50: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
50: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
50: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
50: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
50: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
50: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
50: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
50: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
50: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
50: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
50: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
50: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
50: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
50: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
50: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
50: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
50: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
50: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
50: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
50: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
50: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
50: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
50: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
50: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
50: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
50: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
50: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
50: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (74 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (3 ms)
50: [----------] 2 tests from DumpTest (77 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms)
50: [----------] 3 tests from HelpwritingTest (3 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -1099105283
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (2 ms)
50: [----------] 4 tests from ReportMethodsTest (4 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (8 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (5 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (6 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (37 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (15 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (2072 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 2.10 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (0 ms)
51: [----------] 4 tests from Checkpoint (1 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (2 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
51: [----------] 2 tests from FileMD5Test (3 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (6 ms)
51: [----------] 3 tests from MrcSerializer (6 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
51: [----------] 4 tests from MrcDensityMap (9 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (0 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
51: [----------] 2 tests from TngTest (0 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms)
51: [----------] 4 tests from XvgioTest (2 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (9 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (32 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.06 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 193 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
52: [----------] 15 tests from IndexBlockTest (7 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
52: [----------] 11 tests from IndexMapTest (5 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (36 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (33 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (25 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (10 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (99 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (228 ms total)
52:
52: [----------] 13 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex
52: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
52: [----------] 13 tests from PositionCalculationTest (7 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
52: [----------] 29 tests from SelectionCollectionTest (40 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (25 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (17 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (13 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (15 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (10 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (10 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (13 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (5 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (340 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms)
52: [----------] 17 tests from SelectionOptionTest (15 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
52: [----------] 9 tests from SelectionFileOptionTest (8 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 193 tests from 11 test cases ran. (676 ms total)
52: [ PASSED ] 193 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 0.71 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: [ OK ] MdrunTest.WritesHelp (37 ms)
53: [----------] 1 test from MdrunTest (37 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -67375105
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.252 0.126 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.367 17.562
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (158 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -1836361
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.234 0.117 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.472 16.299
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (150 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -809017354
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.273 0.137 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.264 18.988
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (167 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (476 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.230 0.115 199.4
53: (ns/day) (hour/ns)
53: Performance: 12.755 1.882
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (153 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.261 0.131 199.6
53: (ns/day) (hour/ns)
53: Performance: 11.235 2.136
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (159 ms)
53: [----------] 2 tests from Argon12/OutputFiles (312 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -74459265
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.209 0.105 199.2
53: (ns/day) (hour/ns)
53: Performance: 5.770 4.159
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (137 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 2144860159
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.258 0.129 199.3
53: (ns/day) (hour/ns)
53: Performance: 4.674 5.135
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (161 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -1610613250
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.194 0.097 199.2
53: (ns/day) (hour/ns)
53: Performance: 6.220 3.858
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (139 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (437 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -813241891
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.221 0.111 199.3
53: (ns/day) (hour/ns)
53: Performance: 2.340 10.259
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (141 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -4270213
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.198 0.099 199.1
53: (ns/day) (hour/ns)
53: Performance: 2.613 9.185
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (141 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to 1573873023
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.188 0.095 199.1
53: (ns/day) (hour/ns)
53: Performance: 2.741 8.756
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (136 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (419 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (1798 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 1.82 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -4823057
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (32 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.8208447e+03
54: Maximum force = 4.7331094e+03 on atom 2
54: Norm of force = 1.7801224e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -73749
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (30 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (18 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.7604385e+03
54: Maximum force = 4.6344800e+03 on atom 2
54: Norm of force = 1.7575605e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1872280363
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (29 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (17 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -204477825
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (28 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.7138666e+04
54: Maximum force = 4.3409717e+03 on atom 2
54: Norm of force = 1.2549793e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -142677516
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (29 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to -17309861
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (20 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to 1451196127
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.191 0.096 199.3
54: (ns/day) (hour/ns)
54: Performance: 2.707 8.866
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.228 0.114 199.4
54: (ns/day) (hour/ns)
54: Performance: 3.786 6.339
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (249 ms)
54: [----------] 9 tests from DensityFittingTest (453 ms total)
54:
54: [----------] 4 tests from MimicTest
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 182.7
54: (ns/day) (hour/ns)
54: Performance: 60.237 0.398
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2147477294
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (29 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.002 182.8
54: (ns/day) (hour/ns)
54: Performance: 56.089 0.428
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2045769093
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (31 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 183.0
54: (ns/day) (hour/ns)
54: Performance: 59.011 0.407
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2138799487
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (30 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 182.1
54: (ns/day) (hour/ns)
54: Performance: 62.106 0.386
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -35239427
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (69 ms)
54: [----------] 4 tests from MimicTest (161 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 59137.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -4328257
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.263 0.132 199.3
54: (ns/day) (hour/ns)
54: Performance: 3.935 6.099
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (561 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 50989.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.1977063e+03
54: Maximum force = 1.7794877e+04 on atom 9
54: Norm of force = 7.8732901e+03
54: Setting the LD random seed to -805472330
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (478 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (1040 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (1738 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 1.76 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -805355555
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (16 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -537139209
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (14 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -34668725
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (14 ms)
55: [----------] 3 tests from GromppTest (45 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -167841825
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.3
55: (ns/day) (hour/ns)
55: Performance: 2.507 9.574
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.188 0.095 199.3
55: (ns/day) (hour/ns)
55: Performance: 2.741 8.756
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (239 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to -92417041
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.192 0.096 199.2
55: (ns/day) (hour/ns)
55: Performance: 2.692 8.917
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.173 0.087 199.2
55: (ns/day) (hour/ns)
55: Performance: 100.355 0.239
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (225 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -315233105
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.157 0.079 199.0
55: (ns/day) (hour/ns)
55: Performance: 3.294 7.287
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.172 0.086 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.001 7.998
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.181 0.091 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.856 8.403
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.187 0.094 199.6
55: (ns/day) (hour/ns)
55: Performance: 2.763 8.685
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.001 0.001 155.2
55: (ns/day) (hour/ns)
55: Performance: 101.938 0.235
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (437 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -541081857
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.184 0.093 199.2
55: (ns/day) (hour/ns)
55: Performance: 2.801 8.569
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.190 0.095 199.2
55: (ns/day) (hour/ns)
55: Performance: 4.533 5.295
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (228 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1572566972
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.179 0.090 199.2
55: (ns/day) (hour/ns)
55: Performance: 2.883 8.323
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (119 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -373571614
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.172 0.087 199.1
55: (ns/day) (hour/ns)
55: Performance: 2.993 8.018
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.172 0.086 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.010 7.974
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (213 ms)
55: [----------] 6 tests from MdrunTerminationTest (1462 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.241 1.685
55: trr version: GMX_trn_file (single precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (132 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.5
55: (ns/day) (hour/ns)
55: Performance: 14.994 1.601
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (126 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (259 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.4
55: (ns/day) (hour/ns)
55: Performance: 13.618 1.762
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.214 0.107 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.243 3.314
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.228 0.115 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.787 3.536
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (398 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.210 0.105 199.5
55: (ns/day) (hour/ns)
55: Performance: 13.975 1.717
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.231 0.116 199.6
55: (ns/day) (hour/ns)
55: Performance: 6.715 3.574
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.187 0.094 199.0
55: (ns/day) (hour/ns)
55: Performance: 8.264 2.904
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (383 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.4
55: (ns/day) (hour/ns)
55: Performance: 14.000 1.714
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.198 0.099 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.829 3.065
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.194 0.097 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.997 3.001
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (365 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.4
55: (ns/day) (hour/ns)
55: Performance: 13.767 1.743
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.214 0.107 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.257 3.307
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.819 3.520
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (392 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.206 1.689
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.272 3.300
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.178 0.089 199.2
55: (ns/day) (hour/ns)
55: Performance: 8.723 2.751
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (367 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.4
55: (ns/day) (hour/ns)
55: Performance: 14.044 1.709
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.214 0.107 199.5
55: (ns/day) (hour/ns)
55: Performance: 7.237 3.316
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.226 0.113 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.865 3.496
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (391 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.208 0.105 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.052 1.708
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.246 0.123 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.306 3.806
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.211 0.106 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.362 3.260
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (399 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.242 0.121 199.5
55: (ns/day) (hour/ns)
55: Performance: 12.122 1.980
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.288 3.293
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.178 0.089 199.3
55: (ns/day) (hour/ns)
55: Performance: 8.727 2.750
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (383 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.0
55: (ns/day) (hour/ns)
55: Performance: 13.955 1.720
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.830 3.514
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.957 3.450
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (502 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.217 0.109 199.1
55: (ns/day) (hour/ns)
55: Performance: 13.499 1.778
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.225 0.113 199.0
55: (ns/day) (hour/ns)
55: Performance: 6.885 3.486
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.204 0.102 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.599 3.158
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (500 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.236 0.118 199.2
55: (ns/day) (hour/ns)
55: Performance: 12.420 1.932
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.243 0.122 198.7
55: (ns/day) (hour/ns)
55: Performance: 6.357 3.775
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.222 0.112 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.966 3.445
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (600 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.208 0.104 199.1
55: (ns/day) (hour/ns)
55: Performance: 14.087 1.704
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.248 0.124 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.251 3.840
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.207 0.104 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.475 3.211
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (575 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5258 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.1
55: (ns/day) (hour/ns)
55: Performance: 11.026 2.177
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.274 0.138 199.0
55: (ns/day) (hour/ns)
55: Performance: 5.655 4.244
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.253 0.127 199.0
55: (ns/day) (hour/ns)
55: Performance: 6.126 3.918
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (578 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.312 0.156 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.402 2.553
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.277 0.139 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.609 4.279
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.268 0.135 198.5
55: (ns/day) (hour/ns)
55: Performance: 5.758 4.168
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (618 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.529 0.265 199.6
55: (ns/day) (hour/ns)
55: Performance: 5.541 4.331
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.281 0.141 199.1
55: (ns/day) (hour/ns)
55: Performance: 5.500 4.363
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.262 0.131 199.2
55: (ns/day) (hour/ns)
55: Performance: 5.914 4.058
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (790 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.679 0.340 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.319 5.557
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.267 0.134 199.0
55: (ns/day) (hour/ns)
55: Performance: 5.806 4.133
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.251 0.126 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.179 3.884
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (825 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2811 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.199 0.100 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.683 1.635
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.212 0.106 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.317 3.280
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.194 0.097 199.3
55: (ns/day) (hour/ns)
55: Performance: 8.005 2.998
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (368 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.199 0.100 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.679 1.635
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.233 0.117 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.647 3.611
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.185 0.093 199.2
55: (ns/day) (hour/ns)
55: Performance: 8.379 2.864
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (388 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.245 0.123 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.966 2.006
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.279 0.140 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.552 4.323
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.177 0.089 199.2
55: (ns/day) (hour/ns)
55: Performance: 8.741 2.746
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (419 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.5
55: (ns/day) (hour/ns)
55: Performance: 12.786 1.877
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.218 3.325
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.204 0.102 198.8
55: (ns/day) (hour/ns)
55: Performance: 7.597 3.159
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (392 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.257 0.129 199.6
55: (ns/day) (hour/ns)
55: Performance: 11.418 2.102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.210 3.329
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.204 0.102 198.8
55: (ns/day) (hour/ns)
55: Performance: 7.588 3.163
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (409 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.241 0.121 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.173 1.972
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.259 3.306
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.190 0.095 199.3
55: (ns/day) (hour/ns)
55: Performance: 8.164 2.940
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (390 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2369 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.243 0.122 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.075 1.988
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.939 3.023
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.194 0.097 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.987 3.005
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (384 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.2
55: (ns/day) (hour/ns)
55: Performance: 13.124 1.829
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.198 0.099 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.829 3.066
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.234 0.117 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.622 3.624
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (403 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.216 0.108 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.559 1.770
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.194 0.097 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.988 3.005
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.208 0.104 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.459 3.217
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (379 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.869 1.865
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.212 0.106 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.302 3.287
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.402 3.242
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (391 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.212 0.106 199.5
55: (ns/day) (hour/ns)
55: Performance: 13.816 1.737
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.872 3.049
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.204 0.102 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.590 3.162
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (377 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.120 1.829
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.936 3.024
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.219 0.110 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.072 3.394
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (389 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (2324 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.285 0.143 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.283 2.334
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.233 0.117 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.641 3.614
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.855 4.099
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (481 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.114 1.830
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.219 0.110 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.079 3.390
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.947 3.020
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (397 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.989 1.716
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.255 3.308
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.212 0.106 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.324 3.277
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (383 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.238 0.120 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.286 1.953
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.854 3.056
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.925 3.028
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (387 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.609 1.763
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.208 0.104 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.459 3.217
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.216 0.108 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.179 3.343
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (407 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.235 0.118 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.462 1.926
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.864 3.052
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.211 0.106 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.351 3.265
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (393 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.192 0.097 199.1
55: (ns/day) (hour/ns)
55: Performance: 15.205 1.578
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.861 3.053
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.194 0.097 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.982 3.007
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (358 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.228 0.114 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.864 1.866
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.230 0.116 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.727 3.568
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.958 3.016
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (393 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.276 0.138 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.628 2.258
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.854 3.056
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.178 0.089 199.2
55: (ns/day) (hour/ns)
55: Performance: 8.694 2.761
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (391 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.193 0.097 199.2
55: (ns/day) (hour/ns)
55: Performance: 15.146 1.585
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.214 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.248 3.311
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.817 3.521
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (383 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.5
55: (ns/day) (hour/ns)
55: Performance: 12.798 1.875
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.233 0.117 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.668 3.599
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.219 0.110 198.9
55: (ns/day) (hour/ns)
55: Performance: 7.069 3.395
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (410 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.190 0.095 199.2
55: (ns/day) (hour/ns)
55: Performance: 15.401 1.558
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.180 0.090 199.0
55: (ns/day) (hour/ns)
55: Performance: 8.612 2.787
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.235 0.118 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.599 3.637
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (372 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.644 0.322 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.557 5.267
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.234 0.117 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.631 3.619
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.200 3.333
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (637 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.359 0.180 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.172 2.937
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.242 0.121 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.414 3.742
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.232 0.117 198.9
55: (ns/day) (hour/ns)
55: Performance: 6.662 3.603
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (498 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.228 0.115 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.819 1.872
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.205 0.103 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.532 3.186
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.188 0.094 199.1
55: (ns/day) (hour/ns)
55: Performance: 8.249 2.909
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (390 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.2
55: (ns/day) (hour/ns)
55: Performance: 15.002 1.600
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.860 3.053
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.217 3.325
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (384 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (6675 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.210 0.105 199.2
55: (ns/day) (hour/ns)
55: Performance: 13.937 1.722
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.528 3.188
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.203 0.102 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.620 3.150
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (390 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (392 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -1126285451
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.172 0.086 198.9
55: (ns/day) (hour/ns)
55: Performance: 1.999 12.008
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (117 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 2147216094
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.175 0.088 199.3
55: (ns/day) (hour/ns)
55: Performance: 1.969 12.191
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (123 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 859238263
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.149 0.075 198.8
55: (ns/day) (hour/ns)
55: Performance: 2.310 10.389
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (106 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (346 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (22224 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 22.26 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to -455442709
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.301 0.151 199.3
56: (ns/day) (hour/ns)
56: Performance: 12.575 1.909
56: [ OK ] OriresTest.OriresCanRun (842 ms)
56: [----------] 1 test from OriresTest (842 ms total)
56:
56: [----------] 1 test from CompelTest
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: Removing center of mass motion in the presence of position restraints
56: might cause artifacts. When you are using position restraints to
56: equilibrate a macro-molecule, the artifacts are usually negligible.
56:
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to 1073703407
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.521 1.261 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.028 23.349
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.174 1.087 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.192 20.139
56: [ OK ] CompelTest.SwapCanRun (5716 ms)
56: [----------] 1 test from CompelTest (5716 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.7
56: (ns/day) (hour/ns)
56: Performance: 87.133 0.275
56: Setting the LD random seed to -1646438417
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (24 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.7
56: (ns/day) (hour/ns)
56: Performance: 85.148 0.282
56: Setting the LD random seed to -1761675533
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (30 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 175.9
56: (ns/day) (hour/ns)
56: Performance: 89.967 0.267
56: Setting the LD random seed to -1092812841
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (24 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 175.4
56: (ns/day) (hour/ns)
56: Performance: 94.396 0.254
56: Setting the LD random seed to -235570741
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (27 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 175.2
56: (ns/day) (hour/ns)
56: Performance: 98.502 0.244
56: Setting the LD random seed to 2134900728
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (21 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 175.6
56: (ns/day) (hour/ns)
56: Performance: 97.129 0.247
56: Setting the LD random seed to -155452546
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (28 ms)
56: [----------] 6 tests from BondedInteractionsTest (154 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -258476225
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.275 0.138 199.3
56: (ns/day) (hour/ns)
56: Performance: 32.852 0.731
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (40119 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -1082206723
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.698 0.349 199.8
56: (ns/day) (hour/ns)
56: Performance: 12.982 1.849
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (17077 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (57199 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -889471493
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.259 0.130 199.3
56: (ns/day) (hour/ns)
56: Performance: 3.326 7.215
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -289931587
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.238 0.119 199.2
56: (ns/day) (hour/ns)
56: Performance: 3.622 6.626
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (23752 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -700538897
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.180 0.090 198.9
56: (ns/day) (hour/ns)
56: Performance: 4.779 5.022
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -8770
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.243 0.122 199.3
56: (ns/day) (hour/ns)
56: Performance: 3.543 6.773
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (384 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24137 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to 2062472175
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.292 0.146 199.4
56: (ns/day) (hour/ns)
56: Performance: 2.953 8.128
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1235331401
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.287 0.144 199.4
56: (ns/day) (hour/ns)
56: Performance: 2.997 8.008
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (362 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (364 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (88598 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 88.63 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to -67937026
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.293 0.147 199.5
57: (ns/day) (hour/ns)
57: Performance: 12.355 1.943
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.220 0.110 199.3
57: (ns/day) (hour/ns)
57: Performance: 16.443 1.460
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.228 0.115 199.3
57: (ns/day) (hour/ns)
57: Performance: 15.843 1.515
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10611 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.005 0.003 174.7
57: (ns/day) (hour/ns)
57: Performance: 32.792 0.732
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1094828554
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (68 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.014 0.007 188.5
57: (ns/day) (hour/ns)
57: Performance: 11.541 2.080
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1328161
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (30757 ms)
57: [----------] 3 tests from PmeTest (41438 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (41470 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 41.49 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 58 tests from 5 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (219 ms)
58: [----------] 1 test from NonbondedBenchTest (219 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.7990997e+01
58: Maximum force = 1.8629761e+02 on atom 13
58: Norm of force = 8.7722009e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2429 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.5862339e+01
58: Maximum force = 4.2727011e+02 on atom 13
58: Norm of force = 1.8452841e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2385 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1937714e+02
58: Maximum force = 9.9988643e+03 on atom 9
58: Norm of force = 4.6166996e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (439 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5174377e+02
58: Maximum force = 7.4208838e+03 on atom 9
58: Norm of force = 3.5693005e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (424 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.5698413e+02
58: Maximum force = 4.5704984e+02 on atom 17
58: Norm of force = 1.8327747e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (74 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06801e+03 on atom 28
58: F-Norm = 4.26916e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.6941180e+02
58: Maximum force = 2.1832491e+02 on atom 17
58: Norm of force = 7.9220732e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (75 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5826 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.7425699e-01
58: Maximum force = 4.0132303e+00 on atom 1
58: Norm of force = 1.6383944e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (26 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (26 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (26 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1939697e+02
58: Maximum force = 9.9704248e+03 on atom 9
58: Norm of force = 4.6227540e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (434 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5625757e+02
58: Maximum force = 7.5018242e+03 on atom 9
58: Norm of force = 3.6139019e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (424 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.6111725e+02
58: Maximum force = 1.2685491e+04 on atom 10
58: Norm of force = 6.0643622e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (429 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1365 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.240 0.120 199.4
58: (ns/day) (hour/ns)
58: Performance: 12.198 1.968
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (single precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.057 0.029 198.9
58: (ns/day) (hour/ns)
58: Performance: 51.022 0.470
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (194 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.207 0.104 199.6
58: (ns/day) (hour/ns)
58: Performance: 14.146 1.697
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.009 0.005 193.2
58: (ns/day) (hour/ns)
58: Performance: 299.756 0.080
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (150 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.204 0.102 199.3
58: (ns/day) (hour/ns)
58: Performance: 14.348 1.673
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.1
58: (ns/day) (hour/ns)
58: Performance: 283.559 0.085
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (151 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.202 0.101 199.4
58: (ns/day) (hour/ns)
58: Performance: 14.499 1.655
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.2
58: (ns/day) (hour/ns)
58: Performance: 280.129 0.086
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (149 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.474 0.237 199.7
58: (ns/day) (hour/ns)
58: Performance: 6.193 3.876
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.2
58: (ns/day) (hour/ns)
58: Performance: 277.279 0.087
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2767 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.279 0.140 199.6
58: (ns/day) (hour/ns)
58: Performance: 10.494 2.287
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 194.8
58: (ns/day) (hour/ns)
58: Performance: 224.544 0.107
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2679 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.215 0.108 199.3
58: (ns/day) (hour/ns)
58: Performance: 13.612 1.763
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 197.6
58: (ns/day) (hour/ns)
58: Performance: 95.850 0.250
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2638 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.268 0.135 199.5
58: (ns/day) (hour/ns)
58: Performance: 10.920 2.198
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.1
58: (ns/day) (hour/ns)
58: Performance: 271.631 0.088
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2586 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.250 0.126 199.2
58: (ns/day) (hour/ns)
58: Performance: 11.683 2.054
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 195.4
58: (ns/day) (hour/ns)
58: Performance: 172.185 0.139
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (229 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.222 0.112 199.1
58: (ns/day) (hour/ns)
58: Performance: 13.170 1.822
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 195.2
58: (ns/day) (hour/ns)
58: Performance: 167.964 0.143
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (218 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.216 0.109 199.1
58: (ns/day) (hour/ns)
58: Performance: 13.530 1.774
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 195.1
58: (ns/day) (hour/ns)
58: Performance: 167.139 0.144
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (266 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.225 0.113 199.2
58: (ns/day) (hour/ns)
58: Performance: 13.034 1.841
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 195.2
58: (ns/day) (hour/ns)
58: Performance: 165.705 0.145
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (250 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (12278 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.309 0.155 199.2
58: (ns/day) (hour/ns)
58: Performance: 9.486 2.530
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.033 0.017 195.4
58: (ns/day) (hour/ns)
58: Performance: 87.358 0.275
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (280 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.295 0.148 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.925 2.418
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.7
58: (ns/day) (hour/ns)
58: Performance: 142.563 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (261 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.289 0.145 199.2
58: (ns/day) (hour/ns)
58: Performance: 10.112 2.373
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.7
58: (ns/day) (hour/ns)
58: Performance: 142.277 0.169
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (258 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.255 0.128 199.1
58: (ns/day) (hour/ns)
58: Performance: 11.457 2.095
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.6
58: (ns/day) (hour/ns)
58: Performance: 141.740 0.169
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (242 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.338 0.170 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.647 2.776
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.6
58: (ns/day) (hour/ns)
58: Performance: 142.735 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (284 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.272 0.137 199.2
58: (ns/day) (hour/ns)
58: Performance: 10.737 2.235
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.4
58: (ns/day) (hour/ns)
58: Performance: 140.157 0.171
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (249 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.273 0.137 199.1
58: (ns/day) (hour/ns)
58: Performance: 10.707 2.242
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.8
58: (ns/day) (hour/ns)
58: Performance: 141.841 0.169
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (250 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.241 0.121 199.1
58: (ns/day) (hour/ns)
58: Performance: 12.120 1.980
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 193.0
58: (ns/day) (hour/ns)
58: Performance: 142.448 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (232 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.258 0.129 199.1
58: (ns/day) (hour/ns)
58: Performance: 11.356 2.113
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.042 0.021 196.3
58: (ns/day) (hour/ns)
58: Performance: 68.434 0.351
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (260 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.271 0.136 199.2
58: (ns/day) (hour/ns)
58: Performance: 10.806 2.221
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 193.1
58: (ns/day) (hour/ns)
58: Performance: 142.709 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (249 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.273 0.137 199.1
58: (ns/day) (hour/ns)
58: Performance: 10.708 2.241
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.9
58: (ns/day) (hour/ns)
58: Performance: 142.841 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (249 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.310 0.155 199.6
58: (ns/day) (hour/ns)
58: Performance: 9.453 2.539
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.021 0.011 192.5
58: (ns/day) (hour/ns)
58: Performance: 136.656 0.176
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (268 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.409 0.205 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.171 3.347
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.7
58: (ns/day) (hour/ns)
58: Performance: 140.154 0.171
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (317 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.290 0.145 199.5
58: (ns/day) (hour/ns)
58: Performance: 10.109 2.374
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.021 0.011 192.8
58: (ns/day) (hour/ns)
58: Performance: 138.012 0.174
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (258 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.308 0.155 199.6
58: (ns/day) (hour/ns)
58: Performance: 9.505 2.525
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.9
58: (ns/day) (hour/ns)
58: Performance: 144.391 0.166
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.263 0.132 199.5
58: (ns/day) (hour/ns)
58: Performance: 11.136 2.155
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.5
58: (ns/day) (hour/ns)
58: Performance: 143.103 0.168
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (242 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.275 0.138 199.4
58: (ns/day) (hour/ns)
58: Performance: 10.659 2.252
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.7
58: (ns/day) (hour/ns)
58: Performance: 140.573 0.171
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (249 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.300 0.151 199.6
58: (ns/day) (hour/ns)
58: Performance: 9.754 2.460
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.9
58: (ns/day) (hour/ns)
58: Performance: 145.328 0.165
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (258 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.296 0.149 199.5
58: (ns/day) (hour/ns)
58: Performance: 9.889 2.427
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.9
58: (ns/day) (hour/ns)
58: Performance: 143.537 0.167
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (259 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.279 0.140 199.5
58: (ns/day) (hour/ns)
58: Performance: 10.490 2.288
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.019 0.010 193.0
58: (ns/day) (hour/ns)
58: Performance: 147.105 0.163
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (249 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.299 0.150 199.5
58: (ns/day) (hour/ns)
58: Performance: 9.811 2.446
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 192.2
58: (ns/day) (hour/ns)
58: Performance: 130.726 0.184
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (262 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.302 0.151 199.6
58: (ns/day) (hour/ns)
58: Performance: 9.699 2.475
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.044 0.022 196.5
58: (ns/day) (hour/ns)
58: Performance: 65.326 0.367
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (283 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.285 0.143 199.2
58: (ns/day) (hour/ns)
58: Performance: 10.259 2.339
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.7
58: (ns/day) (hour/ns)
58: Performance: 140.926 0.170
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (307 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.342 0.171 199.4
58: (ns/day) (hour/ns)
58: Performance: 8.570 2.800
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.011 192.5
58: (ns/day) (hour/ns)
58: Performance: 139.506 0.172
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (319 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.299 0.150 199.2
58: (ns/day) (hour/ns)
58: Performance: 9.782 2.454
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.012 192.8
58: (ns/day) (hour/ns)
58: Performance: 127.188 0.189
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (309 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.306 0.154 199.2
58: (ns/day) (hour/ns)
58: Performance: 9.560 2.510
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 193.0
58: (ns/day) (hour/ns)
58: Performance: 129.888 0.185
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (312 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.697 0.349 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.209 5.702
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.010 192.5
58: (ns/day) (hour/ns)
58: Performance: 139.886 0.172
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (501 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.284 0.143 199.2
58: (ns/day) (hour/ns)
58: Performance: 10.297 2.331
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.021 0.011 193.0
58: (ns/day) (hour/ns)
58: Performance: 133.955 0.179
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (294 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.278 0.140 199.1
58: (ns/day) (hour/ns)
58: Performance: 10.504 2.285
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 193.1
58: (ns/day) (hour/ns)
58: Performance: 129.894 0.185
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (292 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.335 0.168 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.736 2.747
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 193.2
58: (ns/day) (hour/ns)
58: Performance: 127.930 0.188
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (326 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.298 0.150 199.2
58: (ns/day) (hour/ns)
58: Performance: 9.804 2.448
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 193.5
58: (ns/day) (hour/ns)
58: Performance: 128.255 0.187
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.367 0.184 199.4
58: (ns/day) (hour/ns)
58: Performance: 7.977 3.009
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.022 0.011 193.1
58: (ns/day) (hour/ns)
58: Performance: 130.604 0.184
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (341 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.305 0.153 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.597 2.501
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.020 0.011 193.2
58: (ns/day) (hour/ns)
58: Performance: 139.128 0.173
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (305 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (9342 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 58 tests from 5 test cases ran. (29137 ms total)
58: [ PASSED ] 58 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 29.17 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (2677 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2580 ms)
59: [----------] 2 tests from Simple/TpiTest (5258 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (5287 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 5.31 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.004 0.002 264.8
60: (ns/day) (hour/ns)
60: Performance: 54.413 0.441
60: Setting the LD random seed to -1259340293
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (32 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (32 ms total)
60:
60: [----------] 4 tests from MimicTest
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.007 0.002 364.5
60: (ns/day) (hour/ns)
60: Performance: 44.847 0.535
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1213997069
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (32 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.007 0.002 364.9
60: (ns/day) (hour/ns)
60: Performance: 46.061 0.521
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2096095102
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (31 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.007 0.002 366.3
60: (ns/day) (hour/ns)
60: Performance: 45.084 0.532
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -67344386
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (30 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.009 0.002 369.9
60: (ns/day) (hour/ns)
60: Performance: 37.588 0.638
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -810156106
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (79 ms)
60: [----------] 4 tests from MimicTest (175 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from MultiSimTerminationTest (0 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
60:
60: [----------] 3 tests from PmeTest
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to -356089857
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.547 0.137 398.7
60: (ns/day) (hour/ns)
60: Performance: 13.229 1.814
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.428 0.107 398.3
60: (ns/day) (hour/ns)
60: Performance: 16.906 1.420
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.552 0.138 398.8
60: (ns/day) (hour/ns)
60: Performance: 13.115 1.830
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10638 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.010 0.003 344.1
60: (ns/day) (hour/ns)
60: Performance: 30.772 0.780
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -17605155
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (67 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.030 0.008 372.1
60: (ns/day) (hour/ns)
60: Performance: 10.730 2.237
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1078008065
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (30971 ms)
60: [----------] 3 tests from PmeTest (41676 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.7990929e+01
60: Maximum force = 1.8629704e+02 on atom 13
60: Norm of force = 8.7721907e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2489 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.5862312e+01
60: Maximum force = 4.2726910e+02 on atom 13
60: Norm of force = 1.8452761e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2486 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1937704e+02
60: Maximum force = 9.9988633e+03 on atom 9
60: Norm of force = 4.6166993e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (440 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5174442e+02
60: Maximum force = 7.4208892e+03 on atom 9
60: Norm of force = 3.5693002e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (456 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.5698419e+02
60: Maximum force = 4.5704996e+02 on atom 17
60: Norm of force = 1.8327748e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (89 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06801e+03 on atom 28
60: F-Norm = 4.26916e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.6941193e+02
60: Maximum force = 2.1835349e+02 on atom 17
60: Norm of force = 7.9216550e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (141 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (6104 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.7425699e-01
60: Maximum force = 4.0132303e+00 on atom 3
60: Norm of force = 1.6383944e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (46 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.9064207e-01
60: Maximum force = 2.5781622e+00 on atom 3
60: Norm of force = 1.0525302e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (56 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1939685e+02
60: Maximum force = 9.9704248e+03 on atom 9
60: Norm of force = 4.6227568e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (452 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5625764e+02
60: Maximum force = 7.5018237e+03 on atom 9
60: Norm of force = 3.6139019e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (434 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (421 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1423 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (49605 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 49.64 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to 2080214383
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.537 0.135 398.7
61: (ns/day) (hour/ns)
61: Performance: 13.464 1.782
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.475 0.119 398.6
61: (ns/day) (hour/ns)
61: Performance: 15.234 1.575
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.543 0.136 398.7
61: (ns/day) (hour/ns)
61: Performance: 13.316 1.802
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10655 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.010 0.003 341.7
61: (ns/day) (hour/ns)
61: Performance: 30.865 0.778
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1149239882
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (67 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.029 0.008 372.9
61: (ns/day) (hour/ns)
61: Performance: 11.071 2.168
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -105021509
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (30804 ms)
61: [----------] 3 tests from PmeTest (41526 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (41552 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 41.57 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.321 1.948
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.136 1.978
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.105 0.106 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.882 1.729
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.107 0.108 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.630 1.761
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.101 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.579 1.646
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.100 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.706 1.632
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (812 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (812 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.7
62: (ns/day) (hour/ns)
62: Performance: 13.122 1.829
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.102 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.355 1.672
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.105 0.106 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.894 1.727
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.098 0.098 99.4
62: (ns/day) (hour/ns)
62: Performance: 14.968 1.603
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.813 1.620
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.091 0.092 99.4
62: (ns/day) (hour/ns)
62: Performance: 15.967 1.503
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (763 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.818 1.737
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.118 0.118 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.423 1.932
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.011 1.845
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.104 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.104 1.702
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.098 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.870 1.614
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.747 1.746
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (808 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.096 0.096 99.6
62: (ns/day) (hour/ns)
62: Performance: 15.250 1.574
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.102 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.373 1.670
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.231 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.359 3.774
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.139 0.139 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.553 2.274
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.100 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.632 1.640
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.101 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.571 1.647
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (924 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.136 0.136 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.785 2.225
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.140 0.141 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.440 2.299
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.087 0.088 99.4
62: (ns/day) (hour/ns)
62: Performance: 16.773 1.431
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.141 1.977
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.747 1.746
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.098 0.098 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.918 1.609
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (851 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.104 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.068 1.706
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.100 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.692 1.634
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.096 0.096 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.274 1.571
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.105 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.053 1.708
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.116 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.650 1.897
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.098 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.875 1.613
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (783 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.151 0.151 99.8
62: (ns/day) (hour/ns)
62: Performance: 9.730 2.467
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.100 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.619 1.642
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.105 0.105 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.985 1.716
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.098 1.832
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.838 1.734
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.968 2.005
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (867 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.100 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.756 1.626
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.103 99.4
62: (ns/day) (hour/ns)
62: Performance: 14.308 1.677
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.107 0.108 99.4
62: (ns/day) (hour/ns)
62: Performance: 13.596 1.765
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.103 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.311 1.677
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.790 1.740
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.817 1.737
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (809 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.103 0.103 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.265 1.682
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.669 1.894
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.110 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.385 1.793
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.104 99.4
62: (ns/day) (hour/ns)
62: Performance: 14.089 1.704
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.096 0.097 99.4
62: (ns/day) (hour/ns)
62: Performance: 15.152 1.584
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.942 2.010
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (824 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.096 0.096 99.6
62: (ns/day) (hour/ns)
62: Performance: 15.320 1.567
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.109 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.424 1.788
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.154 0.154 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.528 2.519
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.017 1.844
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.811 1.620
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.785 1.623
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (832 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.069 1.836
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.823 1.619
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.110 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.365 1.796
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.118 0.119 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.392 1.937
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.797 1.740
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.001 1.846
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (834 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.111 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.187 1.820
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.776 1.624
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.109 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.448 1.785
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.110 0.110 99.4
62: (ns/day) (hour/ns)
62: Performance: 13.326 1.801
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.113 0.113 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.975 1.850
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.137 1.977
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (842 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.103 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.324 1.676
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.100 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.724 1.630
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.103 0.103 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.241 1.685
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.111 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.210 1.817
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.097 0.097 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.111 1.588
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.989 2.002
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (808 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.104 99.7
62: (ns/day) (hour/ns)
62: Performance: 14.142 1.697
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.101 0.101 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.522 1.653
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.137 0.137 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.690 2.245
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.103 0.103 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.232 1.686
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.790 1.740
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.097 0.097 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.125 1.587
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (816 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.7
62: (ns/day) (hour/ns)
62: Performance: 13.104 1.832
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.117 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.503 1.920
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.103 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.265 1.682
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.112 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.169 1.822
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.097 0.098 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.025 1.597
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.097 0.098 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.059 1.594
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (808 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.103 0.103 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.247 1.685
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.099 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.795 1.622
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.597 2.070
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.301 0.301 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.872 4.926
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.169 0.170 99.7
62: (ns/day) (hour/ns)
62: Performance: 8.647 2.776
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.823 1.736
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1090 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.100 0.100 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.703 1.632
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.097 0.097 99.5
62: (ns/day) (hour/ns)
62: Performance: 15.090 1.590
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.099 0.100 99.5
62: (ns/day) (hour/ns)
62: Performance: 14.716 1.631
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.108 0.108 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.607 1.764
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.111 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.184 1.820
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.118 99.4
62: (ns/day) (hour/ns)
62: Performance: 12.440 1.929
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (810 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.128 99.8
62: (ns/day) (hour/ns)
62: Performance: 11.439 2.098
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.101 0.101 99.7
62: (ns/day) (hour/ns)
62: Performance: 14.512 1.654
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.105 99.7
62: (ns/day) (hour/ns)
62: Performance: 14.032 1.710
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.096 0.096 99.7
62: (ns/day) (hour/ns)
62: Performance: 15.222 1.577
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.8
62: (ns/day) (hour/ns)
62: Performance: 12.750 1.882
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.114 0.114 99.8
62: (ns/day) (hour/ns)
62: Performance: 12.833 1.870
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (824 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.104 0.104 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.105 1.702
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.020 1.843
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.128 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.510 2.085
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.135 0.136 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.829 2.216
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.139 0.140 99.5
62: (ns/day) (hour/ns)
62: Performance: 10.528 2.280
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.131 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.218 2.139
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (923 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.122 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.004 1.999
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.592 2.070
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.122 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.029 1.995
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.995 1.847
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.4
62: (ns/day) (hour/ns)
62: Performance: 11.979 2.003
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.130 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.270 2.130
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (900 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.199 2.143
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.136 0.136 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.765 2.229
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.243 2.135
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.743 1.883
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.673 2.056
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.696 2.052
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (916 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.156 0.157 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.366 2.562
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.175 0.176 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.364 2.869
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.146 0.147 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.001 2.400
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.132 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.148 2.153
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.740 1.884
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.123 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.884 2.019
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1009 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.308 2.122
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.329 1.947
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.138 0.138 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.618 2.260
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.130 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.265 2.130
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.116 0.117 99.4
62: (ns/day) (hour/ns)
62: Performance: 12.563 1.910
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.140 0.141 99.5
62: (ns/day) (hour/ns)
62: Performance: 10.433 2.300
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (933 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.122 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.030 1.995
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.321 1.948
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.791 1.740
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.132 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.155 2.151
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.134 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.956 2.191
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.703 2.051
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (890 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.139 0.140 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.505 2.285
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.118 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.456 1.927
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.106 1.831
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.086 1.834
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.190 0.190 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.729 3.105
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.131 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.174 2.148
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (967 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.194 2.144
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.152 0.152 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.637 2.490
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.743 1.883
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.110 0.110 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.301 1.804
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.134 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.960 2.190
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.576 2.073
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (928 ms)
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (21765 ms total)
62:
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.167 0.167 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.771 2.736
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.116 0.116 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.664 1.895
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.144 0.145 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.136 2.368
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.130 99.4
62: (ns/day) (hour/ns)
62: Performance: 11.273 2.129
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.357 0.357 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.110 5.840
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.144 0.144 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.201 2.353
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (15948 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.127 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.560 2.076
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.161 0.162 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.087 2.641
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.125 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.711 2.049
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.694 2.052
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.122 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.077 1.987
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.107 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.755 1.745
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (15711 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.209 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.037 3.411
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.143 0.143 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.238 2.344
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.688 2.053
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.770 1.879
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.109 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.432 1.787
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.134 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.945 2.193
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (15596 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.149 0.149 99.8
62: (ns/day) (hour/ns)
62: Performance: 9.845 2.438
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.134 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.942 2.193
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.143 0.144 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.208 2.351
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.118 0.119 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.350 1.943
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.133 0.134 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.000 2.182
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.163 0.164 99.6
62: (ns/day) (hour/ns)
62: Performance: 8.958 2.679
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (15723 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.586 2.072
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.145 0.146 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.085 2.380
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.133 0.134 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.968 2.188
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.120 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.276 1.955
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.120 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.225 1.963
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.118 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.500 1.920
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (15724 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.134 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.959 2.190
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.125 99.4
62: (ns/day) (hour/ns)
62: Performance: 11.778 2.038
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.137 0.137 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.700 2.243
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.125 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.752 2.042
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.136 0.136 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.783 2.226
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.812 2.032
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (15701 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.334 2.118
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.307 1.950
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.133 0.134 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.966 2.189
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.336 2.117
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.815 2.031
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.128 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.479 2.091
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (15893 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.114 0.115 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.823 1.872
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.125 0.126 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.678 2.055
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.009 1.845
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.827 2.029
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.138 0.138 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.614 2.261
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.128 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.507 2.086
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (15815 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.147 0.148 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.941 2.414
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.551 2.078
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.118 99.4
62: (ns/day) (hour/ns)
62: Performance: 12.444 1.929
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.184 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.972 3.010
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.143 1.977
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.112 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.119 1.829
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (15751 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.143 0.143 99.8
62: (ns/day) (hour/ns)
62: Performance: 10.262 2.339
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.136 0.136 99.8
62: (ns/day) (hour/ns)
62: Performance: 10.781 2.226
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.8
62: (ns/day) (hour/ns)
62: Performance: 12.722 1.886
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.128 99.8
62: (ns/day) (hour/ns)
62: Performance: 11.450 2.096
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.121 99.8
62: (ns/day) (hour/ns)
62: Performance: 12.161 1.974
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.120 99.8
62: (ns/day) (hour/ns)
62: Performance: 12.207 1.966
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (15669 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.312 1.949
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.132 0.133 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.055 2.171
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.138 0.139 99.5
62: (ns/day) (hour/ns)
62: Performance: 10.568 2.271
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.697 1.890
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.131 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.172 2.148
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.207 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.099 3.381
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (15819 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.151 0.152 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.689 2.477
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.140 0.140 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.463 2.294
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.134 0.135 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.894 2.203
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.127 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.587 2.071
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.137 0.137 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.694 2.244
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.214 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.855 3.501
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (16166 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.267 2.130
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.129 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.401 2.105
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.139 0.140 99.6
62: (ns/day) (hour/ns)
62: Performance: 10.508 2.284
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.4
62: (ns/day) (hour/ns)
62: Performance: 11.949 2.009
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.173 0.174 99.7
62: (ns/day) (hour/ns)
62: Performance: 8.446 2.842
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.125 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.776 2.038
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (15865 ms)
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (205384 ms total)
62:
62: [----------] Global test environment tear-down
62: [==========] 39 tests from 3 test cases ran. (228043 ms total)
62: [ PASSED ] 39 tests.
62/65 Test #62: MdrunMpiCoordinationTestsOneRank ...... Passed 228.08 sec
test 63
Start 63: MdrunMpiCoordinationTestsTwoRanks
63: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
63: Test timeout computed to be: 1920
63: [==========] Running 39 tests from 3 test cases.
63: [----------] Global test environment set-up.
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest
63: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.266 0.134 199.2
63: (ns/day) (hour/ns)
63: Performance: 10.993 2.183
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.230 0.116 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.683 1.892
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.8
63: (ns/day) (hour/ns)
63: Performance: 13.126 1.828
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.202 0.102 198.7
63: (ns/day) (hour/ns)
63: Performance: 14.469 1.659
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.223 0.112 198.9
63: (ns/day) (hour/ns)
63: Performance: 13.099 1.832
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.104 198.8
63: (ns/day) (hour/ns)
63: Performance: 14.130 1.699
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (856 ms)
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest (856 ms total)
63:
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.232 0.116 199.1
63: (ns/day) (hour/ns)
63: Performance: 12.626 1.901
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.205 0.103 198.4
63: (ns/day) (hour/ns)
63: Performance: 14.198 1.690
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.200 0.100 198.8
63: (ns/day) (hour/ns)
63: Performance: 14.631 1.640
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.118 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.416 1.933
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.257 0.129 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.367 2.111
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.238 0.119 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.294 1.952
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (868 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.236 0.119 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.368 1.940
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.214 0.108 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.608 1.764
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.217 0.109 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.424 1.788
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.214 0.108 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.629 1.761
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.118 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.426 1.931
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.208 0.105 198.3
63: (ns/day) (hour/ns)
63: Performance: 13.980 1.717
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (866 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.243 0.122 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.033 1.995
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.215 0.108 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.580 1.767
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.2
63: (ns/day) (hour/ns)
63: Performance: 13.107 1.831
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.344 0.173 199.1
63: (ns/day) (hour/ns)
63: Performance: 8.512 2.819
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.220 0.111 198.1
63: (ns/day) (hour/ns)
63: Performance: 13.245 1.812
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.221 0.111 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.223 1.815
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (917 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.258 0.130 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.316 2.121
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.215 0.108 198.8
63: (ns/day) (hour/ns)
63: Performance: 13.607 1.764
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.227 0.114 198.6
63: (ns/day) (hour/ns)
63: Performance: 12.852 1.867
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.212 0.107 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.767 1.743
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.234 0.118 198.6
63: (ns/day) (hour/ns)
63: Performance: 12.479 1.923
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.220 0.111 198.5
63: (ns/day) (hour/ns)
63: Performance: 13.228 1.814
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (870 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.215 1.965
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.229 0.115 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.746 1.883
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.474 0.238 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.183 3.882
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.362 0.182 199.1
63: (ns/day) (hour/ns)
63: Performance: 8.082 2.969
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.210 0.106 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.873 1.730
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.198 0.100 198.4
63: (ns/day) (hour/ns)
63: Performance: 14.753 1.627
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1050 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.234 1.962
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.5
63: (ns/day) (hour/ns)
63: Performance: 13.122 1.829
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.218 0.110 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.379 1.794
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.317 0.159 198.8
63: (ns/day) (hour/ns)
63: Performance: 9.220 2.603
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.185 0.093 198.4
63: (ns/day) (hour/ns)
63: Performance: 15.713 1.527
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.223 0.112 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.059 1.838
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (895 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.304 0.153 199.2
63: (ns/day) (hour/ns)
63: Performance: 9.621 2.494
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.241 0.121 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.117 1.981
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.238 0.120 198.2
63: (ns/day) (hour/ns)
63: Performance: 12.247 1.960
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.119 198.2
63: (ns/day) (hour/ns)
63: Performance: 12.365 1.941
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.206 0.104 197.9
63: (ns/day) (hour/ns)
63: Performance: 14.143 1.697
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.204 0.103 198.5
63: (ns/day) (hour/ns)
63: Performance: 14.296 1.679
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (899 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.204 0.103 198.7
63: (ns/day) (hour/ns)
63: Performance: 14.300 1.678
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.228 0.114 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.829 1.871
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.233 0.117 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.528 1.916
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.121 198.3
63: (ns/day) (hour/ns)
63: Performance: 12.182 1.970
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.104 198.3
63: (ns/day) (hour/ns)
63: Performance: 14.059 1.707
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.244 0.123 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.965 2.006
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (858 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.210 0.106 199.0
63: (ns/day) (hour/ns)
63: Performance: 13.899 1.727
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.200 0.101 198.8
63: (ns/day) (hour/ns)
63: Performance: 14.569 1.647
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.192 0.097 198.7
63: (ns/day) (hour/ns)
63: Performance: 15.192 1.580
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.275 0.138 199.1
63: (ns/day) (hour/ns)
63: Performance: 10.634 2.257
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.230 0.116 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.710 1.888
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.209 0.105 198.4
63: (ns/day) (hour/ns)
63: Performance: 13.945 1.721
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (824 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.111 198.9
63: (ns/day) (hour/ns)
63: Performance: 13.176 1.822
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.215 0.108 198.8
63: (ns/day) (hour/ns)
63: Performance: 13.588 1.766
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.322 0.162 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.084 2.642
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.190 0.096 198.3
63: (ns/day) (hour/ns)
63: Performance: 15.304 1.568
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.247 0.124 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.836 2.028
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.118 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.428 1.931
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (892 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.227 0.114 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.856 1.867
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.243 0.122 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.019 1.997
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.202 0.102 198.5
63: (ns/day) (hour/ns)
63: Performance: 14.461 1.660
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.227 0.114 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.880 1.863
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.210 0.106 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.866 1.731
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.228 0.114 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.833 1.870
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (849 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.121 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.101 1.983
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.232 0.117 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.574 1.909
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.209 0.105 198.3
63: (ns/day) (hour/ns)
63: Performance: 13.924 1.724
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.225 0.114 198.4
63: (ns/day) (hour/ns)
63: Performance: 12.935 1.855
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.235 1.962
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.206 0.104 198.7
63: (ns/day) (hour/ns)
63: Performance: 14.168 1.694
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (858 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.258 0.130 199.1
63: (ns/day) (hour/ns)
63: Performance: 11.335 2.117
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.230 0.116 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.708 1.889
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.220 0.111 198.8
63: (ns/day) (hour/ns)
63: Performance: 13.247 1.812
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.238 0.120 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.286 1.953
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.209 0.105 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.968 1.718
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.192 0.097 198.4
63: (ns/day) (hour/ns)
63: Performance: 15.197 1.579
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (851 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.256 0.129 199.1
63: (ns/day) (hour/ns)
63: Performance: 11.406 2.104
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.243 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.043 1.993
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.248 0.125 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.785 2.037
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.234 0.118 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.454 1.927
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.208 0.104 198.6
63: (ns/day) (hour/ns)
63: Performance: 14.056 1.708
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.224 0.113 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.037 1.841
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (891 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.205 0.103 198.8
63: (ns/day) (hour/ns)
63: Performance: 14.209 1.689
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.246 0.123 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.902 2.016
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.240 0.120 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.192 1.969
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.237 0.119 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.340 1.945
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.104 198.6
63: (ns/day) (hour/ns)
63: Performance: 14.069 1.706
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.223 0.112 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.112 1.830
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (859 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.236 0.119 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.362 1.941
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.212 0.106 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.795 1.740
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.9
63: (ns/day) (hour/ns)
63: Performance: 13.156 1.824
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.248 0.125 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.761 2.041
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.310 0.156 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.426 2.546
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.225 0.113 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.953 1.853
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (908 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.248 0.125 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.742 2.044
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.359 0.180 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.161 2.941
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.063 1.990
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.087 1.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.247 0.124 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.836 2.028
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.245 0.123 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.934 2.011
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (958 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.256 0.128 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.432 2.099
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.212 0.107 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.734 1.748
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.236 0.119 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.341 1.945
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.221 0.111 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.212 1.817
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.241 0.121 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.104 1.983
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.291 0.146 198.9
63: (ns/day) (hour/ns)
63: Performance: 10.050 2.388
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (908 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.272 0.137 199.0
63: (ns/day) (hour/ns)
63: Performance: 10.747 2.233
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.213 0.107 198.2
63: (ns/day) (hour/ns)
63: Performance: 13.681 1.754
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.218 0.110 198.2
63: (ns/day) (hour/ns)
63: Performance: 13.369 1.795
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.234 0.118 198.2
63: (ns/day) (hour/ns)
63: Performance: 12.449 1.928
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.241 0.121 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.120 1.980
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.226 0.114 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.922 1.857
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (883 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.209 0.106 198.5
63: (ns/day) (hour/ns)
63: Performance: 13.921 1.724
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.231 0.116 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.621 1.902
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.105 198.4
63: (ns/day) (hour/ns)
63: Performance: 14.050 1.708
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.224 0.113 198.5
63: (ns/day) (hour/ns)
63: Performance: 13.017 1.844
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.245 0.123 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.904 2.016
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.246 0.124 198.7
63: (ns/day) (hour/ns)
63: Performance: 11.869 2.022
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (850 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.257 0.129 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.388 2.107
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.232 0.116 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.609 1.903
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.105 198.2
63: (ns/day) (hour/ns)
63: Performance: 14.034 1.710
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.584 0.293 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.012 4.788
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.205 0.103 198.5
63: (ns/day) (hour/ns)
63: Performance: 14.217 1.688
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.227 0.114 198.7
63: (ns/day) (hour/ns)
63: Performance: 12.836 1.870
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1033 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.207 0.104 198.7
63: (ns/day) (hour/ns)
63: Performance: 14.131 1.698
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.232 0.117 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.588 1.907
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.118 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.422 1.932
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.238 0.120 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.287 1.953
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.122 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.042 1.993
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.4
63: (ns/day) (hour/ns)
63: Performance: 13.107 1.831
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (868 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.225 0.113 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.983 1.849
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.240 0.121 198.6
63: (ns/day) (hour/ns)
63: Performance: 12.150 1.975
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.214 0.108 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.652 1.758
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.163 1.823
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.226 0.114 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.928 1.856
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.122 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.070 1.988
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (865 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.271 0.136 199.0
63: (ns/day) (hour/ns)
63: Performance: 10.789 2.224
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.243 0.122 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.011 1.998
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.200 0.101 198.5
63: (ns/day) (hour/ns)
63: Performance: 14.545 1.650
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.250 0.126 198.7
63: (ns/day) (hour/ns)
63: Performance: 11.655 2.059
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.221 0.111 198.6
63: (ns/day) (hour/ns)
63: Performance: 13.182 1.821
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.223 0.112 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.109 1.831
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (892 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.223 1.963
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.229 0.115 198.4
63: (ns/day) (hour/ns)
63: Performance: 12.739 1.884
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.219 0.110 198.3
63: (ns/day) (hour/ns)
63: Performance: 13.325 1.801
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.202 0.102 198.2
63: (ns/day) (hour/ns)
63: Performance: 14.408 1.666
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.222 0.112 198.3
63: (ns/day) (hour/ns)
63: Performance: 13.118 1.830
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.209 0.105 198.3
63: (ns/day) (hour/ns)
63: Performance: 13.956 1.720
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (842 ms)
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (22257 ms total)
63:
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.224 0.112 199.0
63: (ns/day) (hour/ns)
63: Performance: 13.069 1.836
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.206 0.104 196.8
63: (ns/day) (hour/ns)
63: Performance: 14.067 1.706
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.211 0.106 198.4
63: (ns/day) (hour/ns)
63: Performance: 13.827 1.736
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.297 0.149 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.858 2.435
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.200 0.101 198.7
63: (ns/day) (hour/ns)
63: Performance: 14.595 1.644
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.236 0.119 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.366 1.941
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (15502 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.216 0.109 198.8
63: (ns/day) (hour/ns)
63: Performance: 13.535 1.773
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.257 0.129 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.353 2.114
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.389 0.195 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.516 3.193
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.261 0.131 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.180 2.147
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.226 0.113 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.947 1.854
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.248 0.125 198.7
63: (ns/day) (hour/ns)
63: Performance: 11.791 2.035
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (15661 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.272 0.136 199.0
63: (ns/day) (hour/ns)
63: Performance: 10.765 2.229
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.260 0.131 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.199 2.143
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.261 0.131 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.172 2.148
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.220 0.111 198.7
63: (ns/day) (hour/ns)
63: Performance: 13.281 1.807
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.265 0.133 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.038 2.174
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.237 0.123 193.0
63: (ns/day) (hour/ns)
63: Performance: 11.982 2.003
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (15560 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.231 0.116 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.660 1.896
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.295 0.148 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.917 2.420
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.269 0.135 198.7
63: (ns/day) (hour/ns)
63: Performance: 10.847 2.213
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.259 0.131 198.7
63: (ns/day) (hour/ns)
63: Performance: 11.249 2.134
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.226 0.114 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.931 1.856
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.242 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.082 1.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (15626 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.283 0.142 199.1
63: (ns/day) (hour/ns)
63: Performance: 10.316 2.327
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.231 0.116 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.659 1.896
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.248 0.125 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.790 2.036
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.284 0.143 198.5
63: (ns/day) (hour/ns)
63: Performance: 10.260 2.339
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.227 0.114 198.2
63: (ns/day) (hour/ns)
63: Performance: 12.848 1.868
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.246 0.124 198.1
63: (ns/day) (hour/ns)
63: Performance: 11.826 2.029
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (15272 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.241 0.121 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.147 1.976
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.243 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.027 1.996
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.294 0.148 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.945 2.413
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.255 0.129 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.425 2.101
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.272 0.137 198.8
63: (ns/day) (hour/ns)
63: Performance: 10.721 2.239
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.244 0.123 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.967 2.005
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (15340 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.267 0.134 199.2
63: (ns/day) (hour/ns)
63: Performance: 10.972 2.187
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.265 0.133 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.028 2.176
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.244 0.122 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.990 2.002
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.268 0.135 198.9
63: (ns/day) (hour/ns)
63: Performance: 10.912 2.199
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.208 0.105 198.8
63: (ns/day) (hour/ns)
63: Performance: 14.051 1.708
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.237 0.120 198.3
63: (ns/day) (hour/ns)
63: Performance: 12.269 1.956
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (15319 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.265 0.133 199.1
63: (ns/day) (hour/ns)
63: Performance: 11.044 2.173
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.244 0.123 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.959 2.007
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.320 0.161 198.8
63: (ns/day) (hour/ns)
63: Performance: 9.120 2.631
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.278 0.140 198.9
63: (ns/day) (hour/ns)
63: Performance: 10.523 2.281
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.264 0.133 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.062 2.170
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.247 0.124 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.809 2.032
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (15427 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.235 0.118 199.0
63: (ns/day) (hour/ns)
63: Performance: 12.413 1.933
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.265 0.133 199.1
63: (ns/day) (hour/ns)
63: Performance: 11.042 2.173
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.282 0.141 199.0
63: (ns/day) (hour/ns)
63: Performance: 10.383 2.312
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.261 0.131 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.174 2.148
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.266 0.134 198.9
63: (ns/day) (hour/ns)
63: Performance: 10.983 2.185
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.265 0.134 198.6
63: (ns/day) (hour/ns)
63: Performance: 10.995 2.183
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (15527 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 198.9
63: (ns/day) (hour/ns)
63: Performance: 12.223 1.963
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.253 0.127 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.572 2.074
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.267 0.134 198.8
63: (ns/day) (hour/ns)
63: Performance: 10.924 2.197
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.283 0.142 198.8
63: (ns/day) (hour/ns)
63: Performance: 10.322 2.325
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.258 0.130 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.339 2.117
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.282 0.142 198.5
63: (ns/day) (hour/ns)
63: Performance: 10.346 2.320
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (15764 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.251 0.126 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.659 2.059
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.247 0.124 198.8
63: (ns/day) (hour/ns)
63: Performance: 11.836 2.028
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.280 0.141 198.9
63: (ns/day) (hour/ns)
63: Performance: 10.420 2.303
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.290 0.146 199.1
63: (ns/day) (hour/ns)
63: Performance: 10.082 2.380
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.264 0.133 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.065 2.169
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.317 0.159 199.1
63: (ns/day) (hour/ns)
63: Performance: 9.215 2.604
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (15371 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.286 0.144 198.4
63: (ns/day) (hour/ns)
63: Performance: 10.204 2.352
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.289 0.145 198.7
63: (ns/day) (hour/ns)
63: Performance: 10.102 2.376
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.314 0.158 198.9
63: (ns/day) (hour/ns)
63: Performance: 9.309 2.578
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.284 0.143 198.7
63: (ns/day) (hour/ns)
63: Performance: 10.265 2.338
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.303 0.152 198.5
63: (ns/day) (hour/ns)
63: Performance: 9.639 2.490
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.253 0.127 198.4
63: (ns/day) (hour/ns)
63: Performance: 11.530 2.081
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (15527 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.253 0.127 199.0
63: (ns/day) (hour/ns)
63: Performance: 11.541 2.080
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.327 0.164 199.2
63: (ns/day) (hour/ns)
63: Performance: 8.948 2.682
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.251 0.126 198.9
63: (ns/day) (hour/ns)
63: Performance: 11.659 2.058
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.275 0.138 198.7
63: (ns/day) (hour/ns)
63: Performance: 10.618 2.260
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.251 0.127 198.6
63: (ns/day) (hour/ns)
63: Performance: 11.600 2.069
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.239 0.120 198.8
63: (ns/day) (hour/ns)
63: Performance: 12.203 1.967
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (15182 ms)
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (201083 ms total)
63:
63: [----------] Global test environment tear-down
63: [==========] 39 tests from 3 test cases ran. (224281 ms total)
63: [ PASSED ] 39 tests.
63/65 Test #63: MdrunMpiCoordinationTestsTwoRanks ..... Passed 224.32 sec
test 64
Start 64: MdrunFEPTests
64: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunfep-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunFEPTests.xml"
64: Test timeout computed to be: 600
64: [==========] Running 10 tests from 1 test case.
64: [----------] Global test environment set-up.
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -402653196
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.712 0.356 199.7
64: (ns/day) (hour/ns)
64: Performance: 5.090 4.716
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision)
64: [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10593 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to 1073405935
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.720 0.360 199.7
64: (ns/day) (hour/ns)
64: Performance: 5.033 4.768
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (476 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 5 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 5 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -270663682
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.683 0.342 199.7
64: (ns/day) (hour/ns)
64: Performance: 5.304 4.525
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (459 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off
64: and vdw_modifier=Force-switch
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 100 steps, 0.1 ps.
64: Setting the LD random seed to -766417
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 2.396 1.199 199.9
64: (ns/day) (hour/ns)
64: Performance: 7.281 3.296
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Reading energy frame 30 time 0.030
Reading energy frame 40 time 0.040
Reading energy frame 50 time 0.050
Reading energy frame 60 time 0.060
Reading energy frame 70 time 0.070
Reading energy frame 80 time 0.080
Reading energy frame 90 time 0.090
Reading energy frame 100 time 0.100
Last energy frame read 100 time 0.100 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (1384 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -3285125
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.822 0.411 199.7
64: (ns/day) (hour/ns)
64: Performance: 4.411 5.441
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (523 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: Removing center of mass motion in the presence of position restraints
64: might cause artifacts. When you are using position restraints to
64: equilibrate a macro-molecule, the artifacts are usually negligible.
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -285753673
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.873 0.437 199.7
64: (ns/day) (hour/ns)
64: Performance: 4.152 5.781
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (562 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to 1467457501
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.443 0.222 199.5
64: (ns/day) (hour/ns)
64: Performance: 8.169 2.938
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (330 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: There were 2 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -79833926
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.477 0.239 199.5
64: (ns/day) (hour/ns)
64: Performance: 7.597 3.159
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (353 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -805451047
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.725 0.363 199.7
64: (ns/day) (hour/ns)
64: Performance: 4.997 4.803
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (465 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -235012116
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.593 0.297 199.6
64: (ns/day) (hour/ns)
64: Performance: 6.103 3.933
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (393 ms)
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest (15561 ms total)
64:
64: [----------] Global test environment tear-down
64: [==========] 10 tests from 1 test case ran. (15588 ms total)
64: [ PASSED ] 10 tests.
64/65 Test #64: MdrunFEPTests ......................... Passed 15.61 sec
test 65
Start 65: MdrunSimulatorComparison
65: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml"
65: Test timeout computed to be: 600
65: [==========] Running 0 tests from 0 test cases.
65: [==========] 0 tests from 0 test cases ran. (0 ms total)
65: [ PASSED ] 0 tests.
65:
65: YOU HAVE 18 DISABLED TESTS
65:
65/65 Test #65: MdrunSimulatorComparison .............. Passed 0.03 sec
100% tests passed, 0 tests failed out of 65
Label Time Summary:
GTest = 828.86 sec*proc (63 tests)
IntegrationTest = 300.07 sec*proc (16 tests)
MpiTest = 543.88 sec*proc (8 tests)
SlowTest = 522.78 sec*proc (8 tests)
UnitTest = 6.01 sec*proc (39 tests)
Total Test time (real) = 829.05 sec
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Consolidate compiler generated dependencies of target argon-forces-integration
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testhelpers.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testsystems.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulatorcomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o
/usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target nblib_test_infrastructure
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp: In function 'bool gmx::test::shouldDoComparison(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::test::ComparisonConditions)':
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp:282:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
282 | static bool shouldDoComparison(ArrayRef<const RVec> values, ComparisonConditions comparisonConditions)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:315:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
315 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:317:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
317 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:376:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
376 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:380:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
380 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:382:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
382 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:430:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
430 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:494:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
494 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:499:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
499 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:501:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
501 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:554:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
554 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:558:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
558 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:560:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
560 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nullptr, step, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function 'virtual void gmx::test::ShakeConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
87 | bool success = constrain_shake(
| ~~~~~~~~~~~~~~~^
88 | nullptr, &shaked, testData->invmass_.data(), *testData->idef_, testData->ir_, testData->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
89 | testData->xPrime_, testData->xPrime2_, nullptr, &testData->nrnb_, testData->lambda_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
90 | &testData->dHdLambda_, testData->invdt_, testData->v_, testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | testData->virialScaled_, false, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function 'virtual void gmx::test::LincsConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
127 | bool success = constrain_lincs(
| ~~~~~~~~~~~~~~~^
128 | false, testData->ir_, 0, lincsd, testData->invmass_.data(), &cr, &ms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
129 | testData->x_.arrayRefWithPadding(), testData->xPrime_.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | testData->xPrime2_.arrayRefWithPadding().unpaddedArrayRef(), pbc.box, &pbc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | testData->hasMassPerturbed_, testData->lambda_, &testData->dHdLambda_, testData->invdt_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
132 | testData->v_.arrayRefWithPadding().unpaddedArrayRef(), testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133 | testData->virialScaled_, gmx::ConstraintVariable::Positions, &testData->nrnb_, maxwarn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 | &warncount_lincs);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasgrid.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target density_fitting_applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/freeenergyparameters.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'static void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target applied_forces-test
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::PaddedVector<T, Allocator>::PaddedVector(const std::initializer_list<_Tp>&) [with T = gmx::BasicVector<double>; Allocator = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target listed_forces-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::LeapFrogHostTestRunner::integrate(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
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[ 69%] Built target onlinehelp-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::{anonymous}::computeDisplacements(gmx::ArrayRef<const int>, const std::vector<gmx::BasicVector<double> >&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'static void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<gmx::BasicVector<double> >&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
198 | cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | lagrangianValues, &numErrors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -MF CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o.d -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mutex.cpp.o -MF CMakeFiles/utility-test.dir/mutex.cpp.o.d -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:80:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
80 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:119:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
119 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:147:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
147 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_availability.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target mdlib-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:340:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
340 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:343:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
343 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:346:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
346 | c_sampleCoordinatesFull.begin() + 16);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:203:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
203 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target ewald-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/template_mp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_buffer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/typecasts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target gpu_utils-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
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/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/checkpointdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::AffineTransformationTest_applyTransformationToVectors_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:215:85: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
215 | const AffineTransformation affineTransformation(transformMatrix, transformVector);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::AffineTransformationTest_identityTransformYieldsSameVectors_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:199:93: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
199 | const AffineTransformation identityTransformation(identityMatrix<real, 3>(), { 0, 0, 0 });
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:91:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
91 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:98:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
98 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:108:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
108 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:118:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
118 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:140:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:150:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
150 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:170:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
170 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:171:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:179:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
179 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:180:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/listoflists.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/range.cpp.o CMakeFiles/utility-test.dir/strconvert.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/template_mp.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target utility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target mdtypes-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
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/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function 'virtual void gmx::test::{anonymous}::COMInPlaceTest_MatrixDefault_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:168:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
168 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | COMShiftType::Molecule);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:182:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
182 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | COMShiftType::Residue);
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::initialCoordinates()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function 'virtual void gmx::test::{anonymous}::ShiftTest_CoordinateShiftWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:195:15: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
195 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinatesWhole()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinates()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function 'virtual void gmx::test::{anonymous}::MatrixTest_transposeWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:174:70: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
174 | const Matrix3x3 transposedAsymmetricMat = transpose(asymmetricMat);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function 'virtual void gmx::test::{anonymous}::MatrixTest_transposeOfSymmetricMatrix_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:189:68: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
189 | const Matrix3x3 transposedSymmetricMat = transpose(symmetricMat);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target pbcutil-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/gammadistribution.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp: In static member function 'static real gmx::test::{anonymous}::NelderMeadSimplexTest::doubleFirstCoordinateValue(gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp:75:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
75 | static real doubleFirstCoordinateValue(ArrayRef<const real> x) { return 2 * x[0]; }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/normaldistribution.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target options-test
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp: In function 'real gmx::test::{anonymous}::mcCormick(gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp:61:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | real mcCormick(ArrayRef<const real> x)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target table-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target pull-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target compat-test
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target topology-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target math-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target pdb2gmx3-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target pdb2gmx2-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target pdb2gmx1-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target coordinateio-test
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:89:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
89 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:108:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
108 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:126:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
126 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function 'static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target mdrun-modules-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target selection-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-simulator-comparison-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-output-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-non-integrator-test
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_IntegratorWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | integrator.integrate(dt, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target nblib-integrator-test
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:44:
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_GmxForceCalculatorCanCompute_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
66 | EXPECT_NO_THROW(gmxForceCalculator->compute(simState.coordinates(), simState.forces()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_SpcMethanolForcesAreCorrect_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
82 | ASSERT_NO_THROW(forceCalculator.compute(simState.coordinates(), forces));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_CanIntegrateSystem_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
119 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
120 | EXPECT_NO_THROW(integrator.integrate(1.0, simState.coordinates(), simState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
121 | simState.forces()));
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_ArgonForcesAreCorrect_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
207 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_ExpectedNumberOfForces_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
99 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_UpdateChangesForces_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
153 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
163 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
175 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
181 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target nblib-integration-test
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float, float, float}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasNan_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasInf_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::StrongType<double, nblib::MassParameter>}; _Tp = nblib::StrongType<double, nblib::MassParameter>; _Alloc = std::allocator<nblib::StrongType<double, nblib::MassParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::StrongType<double, nblib::MassParameter> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasParticleTypeIds_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
In file included from /usr/include/c++/10/map:60,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::tuple<int, int>&&>, std::tuple<>}; _Key = std::tuple<int, int>; _Val = std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >; _KeyOfValue = std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]':
/usr/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::tuple<int, int>; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]':
/usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyListedInteractions_Test::TestBody()':
/usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target nblib-util-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasMasses_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::StrongType<double, nblib::MassParameter>*, std::vector<nblib::StrongType<double, nblib::MassParameter> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyCanAggregateBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:53,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:54:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function 'auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 3>; InteractionType = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
392 | auto computeForces(const std::vector<Index>& indices,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function 'auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 4>; InteractionType = nblib::HarmonicAngleType; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
56 | std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /usr/include/c++/10/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp: In member function 'virtual void nblib::test::{anonymous}::LinearChainDataFixture_Multithreading_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
234 | lfCalculator.compute(x, forces, energies);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /usr/include/c++/10/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'nblib::LinearChainData::LinearChainData(int, float)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target nblib-setup-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::unique_ptr<InteractionDefinitions, std::default_delete<InteractionDefinitions> >, std::unique_ptr<gmx_ffparams_t, std::default_delete<gmx_ffparams_t> > > nblib::createFFparams(const ListedInteractionData&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib-listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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[ 96%] Built target mdrunutility-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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[ 97%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (0 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (0 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms)
1: [----------] 5 tests from NBlibTest (1 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (0 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms)
1: [----------] 5 tests from ListedExampleData (2 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (1 ms)
1: [----------] 1 test from LinearChainDataFixture (1 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (0 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (0 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (2 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (2 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (1 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (12 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 0.04 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.02 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.151648 y 4.370903 z 5.083184
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.02 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (1 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (0 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (1 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms)
4: [----------] 10 tests from NblibTraitsUtils (1 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (2 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.02 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (1 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (0 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (1 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (1 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (1 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (1 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (6 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (6 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.03 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (2 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (0 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (2 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (1 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (1 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (0 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (1 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms)
6: [----------] 19 tests from NBlibTest (11 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (11 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.03 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (1 ms)
7: [----------] 1 test from NBlibTest (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (1 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.02 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (17 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (29 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (2 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (1 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (2 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (1 ms)
8: [----------] 4 tests from XvgTests (6 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (53 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.08 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (2 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.02 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (1 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (1 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (0 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (1 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (1 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
10: [----------] 2 tests from CStringUtilityTest (0 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (1 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (0 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
10: [----------] 6 tests from TreeValueTransformTest (1 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (0 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (0 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (1 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (1 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (1 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (0 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
10: [----------] 7 tests from LoggerTest (4 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (1 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (0 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (1 ms)
10: [----------] 2 tests from PathTest (2 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (0 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (1 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (1 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (0 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (2 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (0 ms)
10: [----------] 1 test from JoinStringsTest (0 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (0 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
10: [----------] 10 tests from TextLineWrapperTest (2 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (1 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (1 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
10: [----------] 6 tests from TextWriterTest (2 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (1 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (40 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.10 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (11 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (13 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (13 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.03 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (1 ms)
12: [----------] 1 test from VerletBufferConstraintTest (1 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (1 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms)
12: [----------] 2 tests from PrEbinTest (1 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (1 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (0 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (0 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (0 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (1 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (0 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (0 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (0 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (1 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms)
12: [----------] 1 test from UpdateGroupsCog (3 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (5 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (8 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (45 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (15 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (14 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (196 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (3 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (1 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (4 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (19 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (7 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (6 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (101 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (4 ms)
12: [----------] 13 tests from WithParameters/SettleTest (34 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (351 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 0.42 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (1 ms)
13: [----------] 1 test from BiasTest (1 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (3 ms)
13: [----------] 1 test from biasGridTest (3 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (6 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (6 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
13: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (13 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (13 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (13 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (13 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (55 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (73 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.10 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (1 ms)
14: [----------] 2 tests from DensityFittingTest (1 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (1 ms)
14: [----------] 1 test from DensityFittingForceProviderState (1 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (5 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.03 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (1 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (0 ms)
15: [----------] 3 tests from ElectricFieldTest (1 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (1 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.02 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (1 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (12 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (15 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (9 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (4 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (8 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (1 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (51 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.10 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (4 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (6 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
17: [----------] 13 tests from CommandLineParserTest (1 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
17: [----------] 3 tests from OutputNamesTest (0 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
17: [----------] 21 tests from ParseCommonArgsTest (7 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (22 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.05 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (1 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
18: [----------] 2 tests from LocalAtomSetManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (2 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.02 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (2 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (12 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (4 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (7 ms)
19: [----------] 4 tests from HaloExchangeTest (25 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (26 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.07 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (5 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (4 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (5 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (6 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (5 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (146 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (71 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (50 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (17 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (29 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (47 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (6 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (52 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (70 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (14 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (15 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (21 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (22 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (10 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (13 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (15 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (19 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (21 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (214 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (703 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 0.81 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (10 ms)
21: [----------] 2 tests from ManyFFTTest (18 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (3 ms)
21: [----------] 1 test from FFTTest (4 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
21: [----------] 1 test from FFFTest3D (3 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (6 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (10 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (26 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (52 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.07 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (0 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (1 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (6 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.06 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (1 ms)
23: [----------] 1 test from CpuInfoTest (1 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: [ OK ] HardwareTopologyTest.Execute (20 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: [ OK ] HardwareTopologyTest.HwlocExecute (18 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (18 ms)
23: [----------] 4 tests from HardwareTopologyTest (76 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (0 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (77 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.10 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (1 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (1 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (1 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (1 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (1 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (73 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (74 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (145 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
24: [----------] 12 tests from DensitySimilarityTest (294 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (0 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (0 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (0 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (1 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (1 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (0 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms)
24: [----------] 21 tests from FunctionTest (5 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (1 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (0 ms)
24: [----------] 9 tests from GaussTransformTest (1 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (0 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (1 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (1 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (0 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (0 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (0 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (0 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (1 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms)
24: [----------] 2 tests from NelderMead (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (1 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (1 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (1 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (1 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (317 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.36 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
25: [----------] 17 tests from ThreadAffinityTest (16 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (17 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.04 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (7 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (18 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (22 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (4 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (17 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (70 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (16 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (33 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (19 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (17 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (5 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (15 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (7 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (113 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (183 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.21 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
27: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (1 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (2 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (0 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (0 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (0 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (0 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (7 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.03 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (8 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (55 ms)
28: [----------] 2 tests from CheckpointDataTest (63 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (0 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (65 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.09 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
29: [----------] 6 tests from TextTableFormatterTest (3 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
29: [----------] 3 tests from HelpManagerTest (1 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
29: [----------] 11 tests from HelpWriterContextTest (5 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (12 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.04 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (2 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (1 ms)
30: [----------] 1 test from OptionsTest (1 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (1 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (2 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (1 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (3 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
30: [----------] 7 tests from TreeValueSupportTest (2 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (25 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.06 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (0 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (0 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms)
31: [----------] 2 tests from MShift (1 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
31: [----------] 1 test from PbcTest (1 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (0 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (17 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (21 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.05 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (1 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (0 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (0 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (2 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (0 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (1 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (0 ms)
32: [----------] 1 test from SeedTest (0 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (0 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (1 ms)
32: [----------] 6 tests from ThreeFry2x64Test (2 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (0 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (0 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (1 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (17 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.05 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (0 ms)
33: [----------] 1 test from RestraintManager (1 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (1 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.02 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (2 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (28 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (56 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (65 ms)
34: [----------] 8 tests from SplineTableTest/0 (160 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (3 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (67 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (136 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (155 ms)
34: [----------] 8 tests from SplineTableTest/1 (371 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (532 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 0.56 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (4 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.03 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
36: [----------] 3 tests from ExclusionBlockTest (1 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (1 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (0 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (1 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (0 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (0 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms)
36: [----------] 13 tests from StringTableTest (8 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms)
36: [----------] 6 tests from LegacySymtabTest (1 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (14 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.04 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (1 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (1 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.02 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (1 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (0 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (6 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (1 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (5 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (13 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.04 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (1 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (1 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (0 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (3 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.03 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
40: [----------] 5 tests from Entropy (1 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (3 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (3 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (2 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (3 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (3 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (3 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (3 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (2 ms)
40: [----------] 10 tests from MindistTest (28 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (4 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
40: [----------] 3 tests from MsdTest (10 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -17304882
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (1153 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -296965
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (1142 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -118075009
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (1038 ms)
40: [----------] 3 tests from MsdMolTest (3333 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (3 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (24 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (3397 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 3.43 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 51 tests from 9 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (4 ms)
41: [----------] 4 tests from GenconfTest (10 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to -134743090
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (1089 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to -2104409
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (1056 ms)
41: [----------] 2 tests from GenionTest (2145 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (5 ms)
41: [----------] 1 test from GenRestrTest (5 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (1 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (5 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (5 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (20 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
41: [----------] 5 tests from InsertMoleculesTest (39 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (11 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (10 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (11 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (8 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (7 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (8 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (6 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (4 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (8 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (9 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (7 ms)
41: [----------] 14 tests from GetIrTest (114 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (20 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (97 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (99 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (48 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (394 ms)
41: [----------] 5 tests from SolvateTest (658 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (1 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 51 tests from 9 test cases ran. (2974 ms total)
41: [ PASSED ] 51 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 3.00 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (181 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (200 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (183 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (167 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (194 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (219 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (203 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (183 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (182 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (204 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (183 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (166 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (195 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (213 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (201 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (183 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (182 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (201 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (183 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (167 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (192 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (211 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (199 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (179 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4573 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (4574 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 4.60 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (130 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (146 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (131 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (123 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (132 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (154 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (137 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (128 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (131 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (149 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (135 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (126 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (136 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (154 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (138 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (127 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2179 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (141 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (158 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (143 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (136 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (145 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (166 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (150 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (142 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (144 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (163 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (146 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (137 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (150 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (168 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (152 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (143 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2387 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (4566 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 4.59 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (181 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (199 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (183 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (162 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (188 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (207 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (195 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (174 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1490 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (65 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (65 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (170 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (188 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (171 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (154 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (180 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (199 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (185 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (169 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1416 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (171 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (128 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (172 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (129 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (171 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (126 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (166 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (130 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (1195 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (84 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (84 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (85 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (86 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (341 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (12854 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (825 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (37239 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (817 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (51736 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (56244 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 56.27 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (16 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (10 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (18 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (26 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (3 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (24 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (27 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (53 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (9 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (27 ms)
45: [----------] 10 tests from AutocorrTest (222 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (2 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (2 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (5 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (13 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (12 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (42 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (8 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (9 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (16 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (39 ms)
45: [----------] 10 tests from ExpfitTest (150 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
45: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (405 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 0.43 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (1 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (24 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (29 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (3 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (35 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (34 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (1 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (4 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (5 ms)
46: [----------] 6 tests from AverageModuleTest (28 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
46: [----------] 2 tests from FrameAverageModuleTest (9 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (14 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (6 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (19 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (5 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 3 tests from BinAverageModuleTest (16 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (10 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (30 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
46: [----------] 3 tests from LifetimeModuleTest (13 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (260 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.29 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (14 ms)
47: [----------] 1 test from OutputSelectorDeathTest (14 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (10 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (16 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (1 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (45 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (0 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (0 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (1 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (1 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (8 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (9 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (8 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (9 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (8 ms)
47: [----------] 5 tests from SetAtomsTest (42 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (0 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (1 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (0 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (8 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (9 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (8 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (50 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (8 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (9 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (26 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (18 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (17 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (72 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (8 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (25 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (9 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (9 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (1 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (8 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (8 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (9 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (8 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (33 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (345 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 0.37 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 85 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (11 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (12 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (14 ms)
48: [----------] 11 tests from AngleModuleTest (132 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (12 ms)
48: [----------] 5 tests from ClustsizeTest (47 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (18 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (127 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (129 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (11 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (12 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (279 ms total)
48:
48: [----------] 6 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (14 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (18 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: Contacts:
48: Number of samples: 2
48: Average distance: 1.00000 nm
48: Standard deviation: 0.00000 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (39 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: SuccessiveContacts:
48: Number of samples: 2
48: Average distance: 1.00000 nm
48: Standard deviation: 0.00000 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (40 ms)
48: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: ManyContacts:
48: Number of samples: 10
48: Average distance: 1.82913 nm
48: Standard deviation: 0.78478 nm
48: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (41 ms)
48: [----------] 6 tests from DistanceModuleTest (170 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (13 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (13 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (26 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (776 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (786 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (1562 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (10 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (9 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (10 ms)
48: [----------] 9 tests from PairDistanceModuleTest (90 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (62 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (44 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (60 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (46 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (71 ms)
48: [----------] 5 tests from RdfModuleTest (283 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (34 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (21 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (17 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms)
48: [----------] 5 tests from SasaModuleTest (132 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (20 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (13 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (15 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (12 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (9 ms)
48: [----------] 8 tests from SelectModuleTest (105 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (3 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (9 ms)
48: [----------] 10 tests from SurfaceAreaTest (29 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (8 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (9 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
48: Setting the LD random seed to 1608120295
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1170 ms)
48: [----------] 4 tests from TopologyInformation (1188 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (11 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (11 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (10 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
48: [----------] 4 tests from TrajectoryModuleTest (42 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (0 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (1 ms)
48: [----------] 5 tests from UnionFinderTest (1 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
48: [----------] 1 test from MappedUnionFinderTest (0 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 85 tests from 16 test cases ran. (4105 ms total)
48: [ PASSED ] 85 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 4.14 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (118 ms)
49: [----------] 1 test from DhdlTest (119 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (266 ms)
49: [----------] 1 test from OriresTest (266 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (31 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (30 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (31 ms)
49: [----------] 3 tests from EnergyTest (93 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (55 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (54 ms)
49: [----------] 2 tests from ViscosityTest (110 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (589 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.61 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -67373601
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = -67373601
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 70158
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
50: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
50: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
50: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
50: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
50: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
50: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
50: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
50: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
50: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
50: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
50: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
50: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
50: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
50: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
50: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
50: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
50: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
50: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
50: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
50: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
50: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
50: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
50: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
50: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
50: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
50: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
50: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
50: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
50: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
50: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (83 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (3 ms)
50: [----------] 2 tests from DumpTest (86 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms)
50: [----------] 3 tests from HelpwritingTest (2 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -46208017
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (2 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms)
50: [----------] 4 tests from ReportMethodsTest (3 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (8 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (6 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (38 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (15 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (2488 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 2.52 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (0 ms)
51: [----------] 4 tests from Checkpoint (0 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (2 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms)
51: [----------] 2 tests from FileMD5Test (2 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (5 ms)
51: [----------] 3 tests from MrcSerializer (6 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (6 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
51: [----------] 4 tests from MrcDensityMap (9 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (1 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (0 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
51: [----------] 2 tests from TngTest (0 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (1 ms)
51: [----------] 4 tests from XvgioTest (2 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (5 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (9 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (31 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.06 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 193 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
52: [----------] 15 tests from IndexBlockTest (3 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
52: [----------] 11 tests from IndexMapTest (5 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (36 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (36 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (21 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (11 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (6 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (101 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (1 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (231 ms total)
52:
52: [----------] 13 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex
52: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms)
52: [----------] 13 tests from PositionCalculationTest (6 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
52: [----------] 29 tests from SelectionCollectionTest (40 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (25 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (17 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (13 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (15 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (10 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (10 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (11 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (13 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (6 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (350 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
52: [----------] 17 tests from SelectionOptionTest (16 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
52: [----------] 9 tests from SelectionFileOptionTest (8 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 193 tests from 11 test cases ran. (687 ms total)
52: [ PASSED ] 193 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 0.72 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: [ OK ] MdrunTest.WritesHelp (37 ms)
53: [----------] 1 test from MdrunTest (38 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -1073905677
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.225 0.113 199.3
53: (ns/day) (hour/ns)
53: Performance: 1.533 15.655
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (144 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -1494499505
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.188 0.094 199.2
53: (ns/day) (hour/ns)
53: Performance: 1.830 13.116
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (123 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -25720125
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.199 0.100 199.3
53: (ns/day) (hour/ns)
53: Performance: 1.727 13.898
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (125 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (393 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.211 0.106 199.3
53: (ns/day) (hour/ns)
53: Performance: 13.848 1.733
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (131 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.232 0.116 199.6
53: (ns/day) (hour/ns)
53: Performance: 12.640 1.899
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (142 ms)
53: [----------] 2 tests from Argon12/OutputFiles (273 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -542771746
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.172 0.087 199.1
53: (ns/day) (hour/ns)
53: Performance: 6.991 3.433
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (117 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -474096225
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.171 0.086 198.9
53: (ns/day) (hour/ns)
53: Performance: 7.050 3.404
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (117 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 905956335
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.183 0.092 199.1
53: (ns/day) (hour/ns)
53: Performance: 6.565 3.656
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (125 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (360 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -553654145
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.157 0.079 198.9
53: (ns/day) (hour/ns)
53: Performance: 3.295 7.284
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (111 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to 764253629
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.150 0.076 198.7
53: (ns/day) (hour/ns)
53: Performance: 3.429 6.999
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (108 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to 1358943583
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.151 0.076 198.8
53: (ns/day) (hour/ns)
53: Performance: 3.421 7.015
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (108 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (327 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (1503 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 1.53 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -33596612
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (34 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.82084736967821e+03
54: Maximum force = 4.73310933913648e+03 on atom 2
54: Norm of force = 1.78012183879532e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1619027268
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (32 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (16 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.76043429797377e+03
54: Maximum force = 4.63447892024619e+03 on atom 2
54: Norm of force = 1.75756003355952e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -2097177
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (29 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (16 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1090669573
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (30 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.71386626596691e+04
54: Maximum force = 4.34097106676756e+03 on atom 2
54: Norm of force = 1.25497916295893e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1146618371
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (33 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to -85479298
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (21 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -807673930
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.157 0.079 199.1
54: (ns/day) (hour/ns)
54: Performance: 3.283 7.310
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.153 0.077 199.1
54: (ns/day) (hour/ns)
54: Performance: 5.608 4.279
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (201 ms)
54: [----------] 9 tests from DensityFittingTest (414 ms total)
54:
54: [----------] 4 tests from MimicTest
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 175.3
54: (ns/day) (hour/ns)
54: Performance: 81.711 0.294
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -100860006
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (25 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 172.3
54: (ns/day) (hour/ns)
54: Performance: 85.793 0.280
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -537245
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (24 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 174.4
54: (ns/day) (hour/ns)
54: Performance: 85.651 0.280
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -69214641
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (24 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.002 182.0
54: (ns/day) (hour/ns)
54: Performance: 56.747 0.423
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 998169850
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (76 ms)
54: [----------] 4 tests from MimicTest (150 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 49229.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -68192778
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.227 0.114 199.2
54: (ns/day) (hour/ns)
54: Performance: 4.556 5.268
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (561 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 55049.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.19770464690297e+03
54: Maximum force = 1.77948604657896e+04 on atom 9
54: Norm of force = 7.87328617833980e+03
54: Setting the LD random seed to -205677602
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (465 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (1026 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (1675 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 1.70 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -1109405730
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (18 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -277885089
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (16 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -105711649
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (17 ms)
55: [----------] 3 tests from GromppTest (53 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -672990310
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.185 0.093 199.1
55: (ns/day) (hour/ns)
55: Performance: 2.784 8.620
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.187 0.094 199.3
55: (ns/day) (hour/ns)
55: Performance: 2.756 8.709
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (232 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to 1070444445
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.174 0.087 199.1
55: (ns/day) (hour/ns)
55: Performance: 2.974 8.070
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.183 0.092 199.2
55: (ns/day) (hour/ns)
55: Performance: 95.148 0.252
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (221 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -1074287617
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.178 0.089 199.2
55: (ns/day) (hour/ns)
55: Performance: 2.900 8.275
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.156 0.078 199.4
55: (ns/day) (hour/ns)
55: Performance: 3.304 7.264
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.150 0.075 199.4
55: (ns/day) (hour/ns)
55: Performance: 3.450 6.957
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.167 0.084 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.088 7.771
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.002 0.001 157.4
55: (ns/day) (hour/ns)
55: Performance: 88.821 0.270
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (420 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -11567140
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.155 0.078 198.9
55: (ns/day) (hour/ns)
55: Performance: 3.327 7.215
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.151 0.076 198.8
55: (ns/day) (hour/ns)
55: Performance: 5.678 4.227
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (202 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1274914479
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.150 0.075 198.9
55: (ns/day) (hour/ns)
55: Performance: 3.436 6.984
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (110 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1575993310
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.151 0.076 199.0
55: (ns/day) (hour/ns)
55: Performance: 3.417 7.023
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.167 0.084 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.101 7.741
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (212 ms)
55: [----------] 6 tests from MdrunTerminationTest (1399 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.207 0.104 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.174 1.693
55: trr version: GMX_trn_file (double precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (137 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.236 0.118 199.6
55: (ns/day) (hour/ns)
55: Performance: 12.414 1.933
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (151 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (288 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.211 0.106 199.4
55: (ns/day) (hour/ns)
55: Performance: 13.860 1.732
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.207 0.104 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.501 3.200
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.541 3.183
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (392 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.282 0.141 199.7
55: (ns/day) (hour/ns)
55: Performance: 10.396 2.309
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.225 0.113 199.6
55: (ns/day) (hour/ns)
55: Performance: 6.911 3.473
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.250 0.125 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.203 3.869
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (459 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.774 1.879
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.959 3.449
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.205 0.103 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.561 3.174
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (406 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.249 0.125 199.5
55: (ns/day) (hour/ns)
55: Performance: 11.761 2.041
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.277 0.139 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.596 4.289
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.224 0.112 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.913 3.472
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (447 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.206 0.103 199.3
55: (ns/day) (hour/ns)
55: Performance: 14.232 1.686
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.231 0.116 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.719 3.572
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.960 3.015
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (383 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.242 0.121 199.6
55: (ns/day) (hour/ns)
55: Performance: 12.100 1.984
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.215 0.108 199.5
55: (ns/day) (hour/ns)
55: Performance: 7.203 3.332
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.425 0.213 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.649 6.578
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (509 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.221 0.111 199.4
55: (ns/day) (hour/ns)
55: Performance: 13.226 1.815
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.279 3.297
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.210 0.105 199.4
55: (ns/day) (hour/ns)
55: Performance: 7.382 3.251
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (391 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.239 0.120 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.264 1.957
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.279 3.297
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.3
55: (ns/day) (hour/ns)
55: Performance: 7.952 3.018
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (392 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.232 0.116 199.1
55: (ns/day) (hour/ns)
55: Performance: 12.610 1.903
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.224 0.112 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.924 3.466
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.237 0.119 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.538 3.671
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (527 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.2
55: (ns/day) (hour/ns)
55: Performance: 12.752 1.882
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.207 0.104 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.483 3.207
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.269 0.135 199.3
55: (ns/day) (hour/ns)
55: Performance: 5.751 4.173
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (534 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.036 2.175
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.220 0.110 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.042 3.408
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.217 0.109 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.137 3.363
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (600 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.253 0.127 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.562 2.076
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.288 0.144 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.389 4.454
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.234 0.117 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.619 3.626
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (616 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5659 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.296 0.149 199.2
55: (ns/day) (hour/ns)
55: Performance: 9.886 2.428
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.163 199.2
55: (ns/day) (hour/ns)
55: Performance: 4.782 5.019
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.279 0.140 198.9
55: (ns/day) (hour/ns)
55: Performance: 5.546 4.328
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (639 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.336 0.169 199.6
55: (ns/day) (hour/ns)
55: Performance: 8.712 2.755
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.273 0.137 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.680 4.225
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.263 0.133 198.6
55: (ns/day) (hour/ns)
55: Performance: 5.866 4.091
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (626 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.306 0.153 199.3
55: (ns/day) (hour/ns)
55: Performance: 9.576 2.506
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.259 0.130 199.0
55: (ns/day) (hour/ns)
55: Performance: 5.975 4.017
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.290 0.145 199.2
55: (ns/day) (hour/ns)
55: Performance: 5.350 4.486
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (689 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.305 0.153 199.2
55: (ns/day) (hour/ns)
55: Performance: 9.605 2.499
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.383 0.192 199.3
55: (ns/day) (hour/ns)
55: Performance: 4.051 5.925
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.328 0.165 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.720 5.084
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (742 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2697 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.295 0.148 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.951 2.412
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.247 0.124 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.272 3.827
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.246 0.123 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.313 3.802
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (459 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.765 1.880
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.232 0.116 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.693 3.586
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.279 0.140 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.566 4.312
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (434 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.241 0.121 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.178 1.971
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.280 0.140 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.536 4.335
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.278 0.139 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.579 4.302
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (466 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.259 0.130 199.5
55: (ns/day) (hour/ns)
55: Performance: 11.308 2.122
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.248 0.124 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.262 3.833
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.220 0.111 198.9
55: (ns/day) (hour/ns)
55: Performance: 7.036 3.411
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (435 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.223 0.112 199.5
55: (ns/day) (hour/ns)
55: Performance: 13.169 1.822
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.231 0.116 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.704 3.580
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.254 0.127 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.100 3.934
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (424 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.222 0.111 199.3
55: (ns/day) (hour/ns)
55: Performance: 13.212 1.816
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.273 3.300
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.815 3.522
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (400 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2618 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.913 1.859
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.213 0.107 199.1
55: (ns/day) (hour/ns)
55: Performance: 7.281 3.296
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.209 0.105 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.408 3.240
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (395 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.251 0.126 199.4
55: (ns/day) (hour/ns)
55: Performance: 11.677 2.055
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.230 0.115 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.748 3.557
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.226 0.113 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.856 3.501
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (426 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.252 0.127 199.4
55: (ns/day) (hour/ns)
55: Performance: 11.608 2.067
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 198.9
55: (ns/day) (hour/ns)
55: Performance: 7.842 3.060
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.211 0.106 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.353 3.264
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (398 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.240 0.120 199.4
55: (ns/day) (hour/ns)
55: Performance: 12.214 1.965
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.247 0.124 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.276 3.824
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.226 0.113 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.857 3.500
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (425 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.293 0.147 199.6
55: (ns/day) (hour/ns)
55: Performance: 9.991 2.402
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.249 0.125 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.236 3.848
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.235 0.118 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.575 3.650
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (460 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.319 0.160 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.187 2.613
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.246 0.123 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.300 3.809
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.244 0.123 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.345 3.783
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (473 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (2577 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.309 0.155 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.495 2.528
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.2
55: (ns/day) (hour/ns)
55: Performance: 5.856 4.099
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.261 0.131 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.939 4.041
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (484 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.284 0.142 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.322 2.325
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.253 0.127 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.116 3.924
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.225 0.113 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.880 3.488
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (459 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.4
55: (ns/day) (hour/ns)
55: Performance: 11.047 2.173
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.233 0.117 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.639 3.615
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.259 0.130 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.979 4.014
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (457 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.317 0.159 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.235 2.599
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.234 0.117 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.622 3.624
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.244 0.122 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.355 3.777
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (474 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.273 0.137 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.734 2.236
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.229 0.115 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.754 3.553
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.242 0.122 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.394 3.754
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (443 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.268 0.134 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.950 2.192
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.248 0.124 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.249 3.840
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.282 0.141 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.496 4.367
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (477 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.276 0.138 199.4
55: (ns/day) (hour/ns)
55: Performance: 10.611 2.262
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.261 0.131 199.4
55: (ns/day) (hour/ns)
55: Performance: 5.932 4.046
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.238 0.119 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.522 3.680
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (474 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.294 0.148 199.5
55: (ns/day) (hour/ns)
55: Performance: 9.951 2.412
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.254 0.128 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.095 3.938
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.254 0.127 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.116 3.924
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (483 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.245 0.123 199.4
55: (ns/day) (hour/ns)
55: Performance: 11.955 2.007
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.244 0.122 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.362 3.772
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.241 0.121 199.4
55: (ns/day) (hour/ns)
55: Performance: 6.426 3.735
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (440 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.233 0.117 199.3
55: (ns/day) (hour/ns)
55: Performance: 12.565 1.910
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.227 0.114 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.832 3.513
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.224 0.112 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.921 3.468
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (416 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.320 0.160 199.6
55: (ns/day) (hour/ns)
55: Performance: 9.165 2.619
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.272 0.136 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.701 4.209
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.259 0.130 199.1
55: (ns/day) (hour/ns)
55: Performance: 5.970 4.020
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (501 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.252 0.126 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.620 2.065
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.246 0.123 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.297 3.811
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.243 0.122 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.386 3.758
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (440 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.250 0.126 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.693 2.052
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.262 0.132 199.2
55: (ns/day) (hour/ns)
55: Performance: 5.908 4.062
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.332 5.540
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (508 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.252 0.126 199.5
55: (ns/day) (hour/ns)
55: Performance: 11.617 2.066
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.265 0.133 199.5
55: (ns/day) (hour/ns)
55: Performance: 5.853 4.101
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.253 0.127 198.9
55: (ns/day) (hour/ns)
55: Performance: 6.108 3.929
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (460 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.212 0.107 199.2
55: (ns/day) (hour/ns)
55: Performance: 13.779 1.742
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.245 0.123 199.2
55: (ns/day) (hour/ns)
55: Performance: 6.323 3.796
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.241 0.121 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.434 3.730
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (423 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (1 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.256 0.128 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.452 2.096
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.238 0.120 199.1
55: (ns/day) (hour/ns)
55: Performance: 6.494 3.696
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.241 0.121 199.3
55: (ns/day) (hour/ns)
55: Performance: 6.435 3.730
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (449 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (7392 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.255 0.128 199.3
55: (ns/day) (hour/ns)
55: Performance: 11.474 2.092
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.195 0.098 199.0
55: (ns/day) (hour/ns)
55: Performance: 7.916 3.032
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.208 0.104 199.2
55: (ns/day) (hour/ns)
55: Performance: 7.461 3.217
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (404 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (404 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 805299711
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.315 0.158 199.5
55: (ns/day) (hour/ns)
55: Performance: 1.096 21.904
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (186 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 1526630363
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.197 0.099 199.4
55: (ns/day) (hour/ns)
55: Performance: 1.747 13.739
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (125 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -1890201733
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.211 0.106 199.2
55: (ns/day) (hour/ns)
55: Performance: 1.633 14.693
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (133 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (444 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (23826 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 23.87 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to 2146806755
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.321 0.161 199.4
56: (ns/day) (hour/ns)
56: Performance: 11.825 2.030
56: [ OK ] OriresTest.OriresCanRun (871 ms)
56: [----------] 1 test from OriresTest (871 ms total)
56:
56: [----------] 1 test from CompelTest
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: Removing center of mass motion in the presence of position restraints
56: might cause artifacts. When you are using position restraints to
56: equilibrate a macro-molecule, the artifacts are usually negligible.
56:
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to -35653123
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 3.119 1.560 199.9
56: (ns/day) (hour/ns)
56: Performance: 0.831 28.889
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.812 1.406 199.9
56: (ns/day) (hour/ns)
56: Performance: 0.922 26.044
56: [ OK ] CompelTest.SwapCanRun (6757 ms)
56: [----------] 1 test from CompelTest (6758 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 177.6
56: (ns/day) (hour/ns)
56: Performance: 82.737 0.290
56: Setting the LD random seed to -10029185
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (25 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.8
56: (ns/day) (hour/ns)
56: Performance: 84.257 0.285
56: Setting the LD random seed to -11540507
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (30 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.6
56: (ns/day) (hour/ns)
56: Performance: 86.509 0.277
56: Setting the LD random seed to -1053317
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (23 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.5
56: (ns/day) (hour/ns)
56: Performance: 87.343 0.275
56: Setting the LD random seed to -696393997
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (27 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 176.8
56: (ns/day) (hour/ns)
56: Performance: 84.374 0.284
56: Setting the LD random seed to -137735937
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (24 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 177.1
56: (ns/day) (hour/ns)
56: Performance: 86.017 0.279
56: Setting the LD random seed to -1096894595
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (30 ms)
56: [----------] 6 tests from BondedInteractionsTest (159 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to 2142075837
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.316 0.158 199.3
56: (ns/day) (hour/ns)
56: Performance: 28.628 0.838
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (252 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -229671
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.388 0.194 199.6
56: (ns/day) (hour/ns)
56: Performance: 23.340 1.028
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (246 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (500 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1309680283
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.268 0.135 199.3
56: (ns/day) (hour/ns)
56: Performance: 3.207 7.484
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -36439
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.258 0.130 199.3
56: (ns/day) (hour/ns)
56: Performance: 3.332 7.203
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (474 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1207964231
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.297 0.149 199.4
56: (ns/day) (hour/ns)
56: Performance: 2.900 8.276
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1611041329
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.235 0.118 199.1
56: (ns/day) (hour/ns)
56: Performance: 3.653 6.569
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (442 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (916 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1124598043
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.354 0.178 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.433 9.865
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to 2128576443
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.333 0.167 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.586 9.281
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (407 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (407 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (9787 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 9.82 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to 1425927550
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.303 0.152 199.5
57: (ns/day) (hour/ns)
57: Performance: 11.928 2.012
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.284 0.142 199.5
57: (ns/day) (hour/ns)
57: Performance: 12.736 1.884
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.241 0.121 199.3
57: (ns/day) (hour/ns)
57: Performance: 15.015 1.598
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (566 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.006 0.003 177.9
57: (ns/day) (hour/ns)
57: Performance: 25.466 0.942
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -407111873
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (75 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.020 0.010 191.0
57: (ns/day) (hour/ns)
57: Performance: 8.448 2.841
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -152338561
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (117 ms)
57: [----------] 3 tests from PmeTest (760 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (787 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 0.81 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 65 tests from 7 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (264 ms)
58: [----------] 1 test from NonbondedBenchTest (266 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.79910463671070e+01
58: Maximum force = 1.86297359432219e+02 on atom 13
58: Norm of force = 8.77219865482161e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2673 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.58622538633290e+01
58: Maximum force = 4.27274822366527e+02 on atom 13
58: Norm of force = 1.84530029253829e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2634 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19376899751521e+02
58: Maximum force = 9.99884921009767e+03 on atom 9
58: Norm of force = 4.61669565054298e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (426 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.51743018140925e+02
58: Maximum force = 7.42089573409111e+03 on atom 9
58: Norm of force = 3.56929298615739e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (439 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.56984193848276e+02
58: Maximum force = 4.56923624626296e+02 on atom 17
58: Norm of force = 1.83258377168331e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (79 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06800e+03 on atom 28
58: F-Norm = 4.26922e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.69410778678185e+02
58: Maximum force = 2.18225948473957e+02 on atom 17
58: Norm of force = 7.92068036537697e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (81 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (6334 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.74257075835450e-01
58: Maximum force = 4.01322929015108e+00 on atom 1
58: Norm of force = 1.63839399694368e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (28 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (28 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (28 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19395484891517e+02
58: Maximum force = 9.97041707197910e+03 on atom 9
58: Norm of force = 4.62274878665467e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (435 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.56258793899479e+02
58: Maximum force = 7.50181017480397e+03 on atom 9
58: Norm of force = 3.61390332564874e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (431 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.61116097794203e+02
58: Maximum force = 1.26854826291223e+04 on atom 10
58: Norm of force = 6.06436286976271e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (445 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1395 ms total)
58:
58: [----------] 5 tests from NormalModesWorks/NormalModesTest
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '2 scaled waters'
58: 12 steps.
58:
58: Maximum force: 9.96989e-06
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.4-Raspbian-2021.4-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Generated 3 of the 3 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (34 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file villin.top, line 2452]:
58: System has non-zero total charge: -2.000000
58: Total charge should normally be an integer. See
58: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
58: for discussion on how close it should be to an integer.
58:
58:
58:
58: Number of degrees of freedom in T-Coupling group System is 765.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=256), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
58: 512 steps.
58:
58: Maximum force: 6.97568e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.4-Raspbian-2021.4-2
58:
58: Diagonalizing to find vectors 7 through 50...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--50 to eigenvec.trr
58: Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 256 Atoms
58: Using begin = 7 and end = 50
58: Full matrix storage format, nrow=768, ncols=768
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (10252 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'flex spc dimer'
58: 12 steps.
58:
58: Maximum force: 3.36401e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.4-Raspbian-2021.4-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (2587 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 6.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=3), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '1 TIP5P'
58: 6 steps.
58:
58: Maximum force: 2.42882e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.4-Raspbian-2021.4-2
58:
58: Diagonalizing to find vectors 7 through 9...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--9 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 3 Atoms
58: There are: 2 VSites
58: Using begin = 7 and end = 9
58: Full matrix storage format, nrow=9, ncols=9
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (2678 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'sw dimer'
58: 12 steps.
58:
58: Maximum force: 1.07599e-03
58: The force is probably not small enough to ensure that you are at a minimum.
58: Be aware that negative eigenvalues may occur
58: when the resulting matrix is diagonalized.
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.4-Raspbian-2021.4-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 6 of the 10 non-bonded parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SW'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: There are: 2 Shells
58: There are: 2 VSites
58:
58: NOTE: in the current version shell prediction during the crun is disabled
58:
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (36 ms)
58: [----------] 5 tests from NormalModesWorks/NormalModesTest (15588 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.234 0.117 199.4
58: (ns/day) (hour/ns)
58: Performance: 12.515 1.918
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (double precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 197.9
58: (ns/day) (hour/ns)
58: Performance: 95.974 0.250
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (181 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.268 0.134 199.6
58: (ns/day) (hour/ns)
58: Performance: 10.925 2.197
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 198.0
58: (ns/day) (hour/ns)
58: Performance: 93.964 0.255
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (198 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.243 0.122 199.5
58: (ns/day) (hour/ns)
58: Performance: 12.045 1.993
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 195.7
58: (ns/day) (hour/ns)
58: Performance: 210.216 0.114
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (176 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.242 0.121 199.5
58: (ns/day) (hour/ns)
58: Performance: 12.097 1.984
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 195.2
58: (ns/day) (hour/ns)
58: Performance: 208.883 0.115
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (175 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.317 0.159 199.5
58: (ns/day) (hour/ns)
58: Performance: 9.236 2.599
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.008 195.3
58: (ns/day) (hour/ns)
58: Performance: 174.724 0.137
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2907 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.323 0.162 199.7
58: (ns/day) (hour/ns)
58: Performance: 9.083 2.642
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.008 195.3
58: (ns/day) (hour/ns)
58: Performance: 176.709 0.136
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2899 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.291 0.146 199.5
58: (ns/day) (hour/ns)
58: Performance: 10.079 2.381
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.037 0.019 198.2
58: (ns/day) (hour/ns)
58: Performance: 78.433 0.306
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2904 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.333 0.167 199.5
58: (ns/day) (hour/ns)
58: Performance: 8.798 2.728
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.037 0.019 197.8
58: (ns/day) (hour/ns)
58: Performance: 79.135 0.303
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2993 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.263 0.132 199.2
58: (ns/day) (hour/ns)
58: Performance: 11.120 2.158
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.029 0.015 196.8
58: (ns/day) (hour/ns)
58: Performance: 100.255 0.239
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (274 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.363 0.182 199.5
58: (ns/day) (hour/ns)
58: Performance: 8.074 2.973
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.027 0.014 196.8
58: (ns/day) (hour/ns)
58: Performance: 108.645 0.221
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (306 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.129 0.565 199.8
58: (ns/day) (hour/ns)
58: Performance: 2.600 9.232
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.029 0.015 196.7
58: (ns/day) (hour/ns)
58: Performance: 100.493 0.239
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (743 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.056 0.528 199.8
58: (ns/day) (hour/ns)
58: Performance: 2.781 8.630
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.028 0.014 195.8
58: (ns/day) (hour/ns)
58: Performance: 103.291 0.232
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (695 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (14453 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.667 0.334 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.394 5.462
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.4
58: (ns/day) (hour/ns)
58: Performance: 95.466 0.251
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (465 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.329 0.165 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.902 2.696
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.4
58: (ns/day) (hour/ns)
58: Performance: 95.353 0.252
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (289 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.410 0.205 199.5
58: (ns/day) (hour/ns)
58: Performance: 7.149 3.357
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 94.354 0.254
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (334 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.330 0.165 199.4
58: (ns/day) (hour/ns)
58: Performance: 8.881 2.702
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.5
58: (ns/day) (hour/ns)
58: Performance: 95.230 0.252
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (290 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.313 0.157 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.353 2.566
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 94.150 0.255
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (284 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.390 0.196 199.4
58: (ns/day) (hour/ns)
58: Performance: 7.501 3.200
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 195.3
58: (ns/day) (hour/ns)
58: Performance: 93.636 0.256
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (326 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.373 0.187 199.4
58: (ns/day) (hour/ns)
58: Performance: 7.845 3.059
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 195.3
58: (ns/day) (hour/ns)
58: Performance: 94.137 0.255
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (316 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.337 0.169 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.686 2.763
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 195.2
58: (ns/day) (hour/ns)
58: Performance: 92.851 0.258
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (301 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.304 0.152 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.640 2.490
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 93.214 0.257
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (282 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.421 0.211 199.5
58: (ns/day) (hour/ns)
58: Performance: 6.958 3.449
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.5
58: (ns/day) (hour/ns)
58: Performance: 93.633 0.256
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (341 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.320 0.161 199.2
58: (ns/day) (hour/ns)
58: Performance: 9.145 2.624
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 195.2
58: (ns/day) (hour/ns)
58: Performance: 94.708 0.253
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (291 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.362 0.181 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.110 2.959
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 195.4
58: (ns/day) (hour/ns)
58: Performance: 94.295 0.255
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (312 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.389 0.195 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.548 3.180
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 195.3
58: (ns/day) (hour/ns)
58: Performance: 93.653 0.256
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (323 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.339 0.170 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.655 2.773
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.032 0.016 195.4
58: (ns/day) (hour/ns)
58: Performance: 89.823 0.267
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (303 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.349 0.175 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.411 2.853
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.032 0.016 194.5
58: (ns/day) (hour/ns)
58: Performance: 90.456 0.265
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.335 0.168 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.741 2.746
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 91.901 0.261
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (298 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.339 0.170 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.656 2.773
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.9
58: (ns/day) (hour/ns)
58: Performance: 91.654 0.262
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (299 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.336 0.168 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.719 2.753
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.033 0.017 195.1
58: (ns/day) (hour/ns)
58: Performance: 86.322 0.278
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (304 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.341 0.171 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.589 2.794
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.034 0.017 195.3
58: (ns/day) (hour/ns)
58: Performance: 85.459 0.281
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.364 0.182 199.6
58: (ns/day) (hour/ns)
58: Performance: 8.050 2.981
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 91.337 0.263
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (319 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.386 0.193 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.593 3.161
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 195.4
58: (ns/day) (hour/ns)
58: Performance: 91.771 0.262
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (332 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.422 0.211 199.7
58: (ns/day) (hour/ns)
58: Performance: 6.958 3.449
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.033 0.017 195.6
58: (ns/day) (hour/ns)
58: Performance: 86.173 0.279
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (347 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.335 0.168 199.4
58: (ns/day) (hour/ns)
58: Performance: 8.739 2.746
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 195.3
58: (ns/day) (hour/ns)
58: Performance: 94.607 0.254
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (328 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.337 0.169 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.694 2.760
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.032 0.016 195.3
58: (ns/day) (hour/ns)
58: Performance: 89.218 0.269
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (335 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.345 0.173 199.3
58: (ns/day) (hour/ns)
58: Performance: 8.492 2.826
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.031 0.016 194.7
58: (ns/day) (hour/ns)
58: Performance: 93.067 0.258
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (341 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.389 0.195 199.4
58: (ns/day) (hour/ns)
58: Performance: 7.530 3.187
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.3
58: (ns/day) (hour/ns)
58: Performance: 95.617 0.251
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (357 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.440 0.221 199.5
58: (ns/day) (hour/ns)
58: Performance: 6.654 3.607
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.6
58: (ns/day) (hour/ns)
58: Performance: 94.895 0.253
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (382 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.426 0.214 199.5
58: (ns/day) (hour/ns)
58: Performance: 6.874 3.491
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.6
58: (ns/day) (hour/ns)
58: Performance: 95.424 0.252
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (375 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.477 0.239 199.5
58: (ns/day) (hour/ns)
58: Performance: 6.140 3.909
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.4
58: (ns/day) (hour/ns)
58: Performance: 95.202 0.252
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (399 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.309 0.155 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.468 2.535
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.016 194.8
58: (ns/day) (hour/ns)
58: Performance: 94.544 0.254
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (317 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.320 0.160 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.162 2.619
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.5
58: (ns/day) (hour/ns)
58: Performance: 95.445 0.251
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (324 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.310 0.155 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.453 2.539
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.4
58: (ns/day) (hour/ns)
58: Performance: 95.880 0.250
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (317 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.322 0.162 199.3
58: (ns/day) (hour/ns)
58: Performance: 9.088 2.641
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.030 0.015 195.2
58: (ns/day) (hour/ns)
58: Performance: 95.599 0.251
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (324 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (10780 ms total)
58:
58: [----------] 2 tests from Angles1/SimpleMdrunTest
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.256 0.128 199.5
58: (ns/day) (hour/ns)
58: Performance: 34.306 0.700
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (162 ms)
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.266 0.133 199.6
58: (ns/day) (hour/ns)
58: Performance: 33.119 0.725
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (166 ms)
58: [----------] 2 tests from Angles1/SimpleMdrunTest (330 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 65 tests from 7 test cases ran. (49305 ms total)
58: [ PASSED ] 65 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 49.38 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (2898 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2795 ms)
59: [----------] 2 tests from Simple/TpiTest (5693 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (5725 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 5.76 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.004 0.002 267.8
60: (ns/day) (hour/ns)
60: Performance: 52.996 0.453
60: Setting the LD random seed to -1073750434
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (32 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (32 ms total)
60:
60: [----------] 4 tests from MimicTest
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.070 0.018 396.0
60: (ns/day) (hour/ns)
60: Performance: 4.920 4.878
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -25405597
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (53 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.006 0.002 359.9
60: (ns/day) (hour/ns)
60: Performance: 49.758 0.482
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1630535507
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (39 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.006 0.002 356.1
60: (ns/day) (hour/ns)
60: Performance: 49.335 0.486
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -621808033
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (37 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.088 0.022 396.6
60: (ns/day) (hour/ns)
60: Performance: 3.877 6.190
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -17931521
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (110 ms)
60: [----------] 4 tests from MimicTest (240 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
60: [----------] 1 test from MultiSimTerminationTest (1 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
60:
60: [----------] 3 tests from PmeTest
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to -1212158787
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.803 0.201 399.1
60: (ns/day) (hour/ns)
60: Performance: 9.019 2.661
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.602 0.151 398.8
60: (ns/day) (hour/ns)
60: Performance: 12.030 1.995
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.834 0.209 399.1
60: (ns/day) (hour/ns)
60: Performance: 8.682 2.764
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (703 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.012 0.003 350.3
60: (ns/day) (hour/ns)
60: Performance: 25.444 0.943
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -540019669
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (78 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.040 0.011 378.8
60: (ns/day) (hour/ns)
60: Performance: 8.214 2.922
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -406880465
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (115 ms)
60: [----------] 3 tests from PmeTest (896 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.79910463671071e+01
60: Maximum force = 1.86297359432220e+02 on atom 13
60: Norm of force = 8.77219865482161e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2858 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.58622538633291e+01
60: Maximum force = 4.27274822366526e+02 on atom 13
60: Norm of force = 1.84530029253829e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2681 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19376899751521e+02
60: Maximum force = 9.99884921009767e+03 on atom 9
60: Norm of force = 4.61669565054298e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (452 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.51743018140926e+02
60: Maximum force = 7.42089573409112e+03 on atom 9
60: Norm of force = 3.56929298615739e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (437 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.56984193848276e+02
60: Maximum force = 4.56923624626296e+02 on atom 17
60: Norm of force = 1.83258377168331e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (102 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06800e+03 on atom 28
60: F-Norm = 4.26922e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.69410778678185e+02
60: Maximum force = 2.18225948474048e+02 on atom 17
60: Norm of force = 7.92068036537643e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (103 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (6635 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.74257075835450e-01
60: Maximum force = 4.01322929015108e+00 on atom 3
60: Norm of force = 1.63839399694368e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (52 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.90642313893957e-01
60: Maximum force = 2.57812909491105e+00 on atom 3
60: Norm of force = 1.05251679559258e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (47 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19395484891518e+02
60: Maximum force = 9.97041707197910e+03 on atom 9
60: Norm of force = 4.62274878665467e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (485 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: NOTE: The number of threads is not equal to the number of (logical) cores
60: and the -pin option is set to auto: will not pin threads to cores.
60: This can lead to significant performance degradation.
60: Consider using -pin on (and -pinoffset in case you run multiple jobs).
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.56258793899479e+02
60: Maximum force = 7.50181017480397e+03 on atom 9
60: Norm of force = 3.61390332564874e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (467 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (420 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1485 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (9471 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 9.51 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to -536936593
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.592 0.148 398.9
61: (ns/day) (hour/ns)
61: Performance: 12.231 1.962
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.520 0.130 398.7
61: (ns/day) (hour/ns)
61: Performance: 13.912 1.725
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.466 0.117 398.5
61: (ns/day) (hour/ns)
61: Performance: 15.500 1.548
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (539 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.012 0.003 352.7
61: (ns/day) (hour/ns)
61: Performance: 24.807 0.967
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1224871969
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (77 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: NOTE: The number of threads is not equal to the number of (logical) cores
61: and the -pin option is set to auto: will not pin threads to cores.
61: This can lead to significant performance degradation.
61: Consider using -pin on (and -pinoffset in case you run multiple jobs).
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.041 0.011 379.4
61: (ns/day) (hour/ns)
61: Performance: 8.087 2.968
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -209917985
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (107 ms)
61: [----------] 3 tests from PmeTest (724 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (749 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 0.77 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.112 99.7
62: (ns/day) (hour/ns)
62: Performance: 13.159 1.824
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.148 0.149 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.883 2.428
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.713 1.888
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.122 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.042 1.993
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.675 1.894
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.107 0.108 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.646 1.759
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (889 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (889 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.118 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.471 1.925
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.110 0.111 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.255 1.811
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.105 0.105 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.975 1.717
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.267 2.130
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.116 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.651 1.897
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.125 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.797 2.034
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (862 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.244 2.134
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.328 1.947
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.162 0.162 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.040 2.655
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.145 0.145 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.119 2.372
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.839 2.027
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.557 3.660
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1069 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.341 2.116
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.127 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.535 2.081
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.144 0.145 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.157 2.363
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.148 1.976
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.132 0.132 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.108 2.161
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.123 0.123 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.909 2.015
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (940 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.340 2.116
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.135 0.136 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.816 2.219
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.107 1.982
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.121 99.5
62: (ns/day) (hour/ns)
62: Performance: 12.110 1.982
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.156 0.157 99.7
62: (ns/day) (hour/ns)
62: Performance: 9.381 2.558
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.194 2.144
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (957 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.113 0.113 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.961 1.852
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.323 1.948
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.122 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.070 1.988
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.129 0.130 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.310 2.122
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.116 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.647 1.898
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.716 1.887
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (875 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.989 2.002
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.110 0.111 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.273 1.808
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.180 1.970
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.102 0.103 99.6
62: (ns/day) (hour/ns)
62: Performance: 14.302 1.678
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.114 0.115 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.793 1.876
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.115 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.757 1.881
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (850 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.154 1.975
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.127 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.542 2.079
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.129 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.426 2.101
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.111 0.112 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.139 1.827
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.117 0.117 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.541 1.914
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.125 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.778 2.038
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (902 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.110 0.110 99.7
62: (ns/day) (hour/ns)
62: Performance: 13.335 1.800
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.131 0.132 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.143 2.154
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.143 0.143 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.267 2.338
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.129 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.419 2.102
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.106 0.106 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.803 1.739
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.123 0.123 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.946 2.009
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (915 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.7
62: (ns/day) (hour/ns)
62: Performance: 13.069 1.836
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.118 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.358 1.942
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.113 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.981 1.849
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.128 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.431 2.100
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.114 0.115 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.827 1.871
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.123 0.123 99.3
62: (ns/day) (hour/ns)
62: Performance: 11.908 2.016
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (875 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.127 0.128 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.517 2.084
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.119 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.318 1.948
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.120 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.209 1.966
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.121 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.090 1.985
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.124 0.124 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.812 2.032
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.130 0.131 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.231 2.137
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (908 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.113 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.049 1.839
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.118 0.119 99.7
62: (ns/day) (hour/ns)
62: Performance: 12.389 1.937
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.093 1.833
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.120 0.121 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.157 1.974
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.115 0.116 99.6
62: (ns/day) (hour/ns)
62: Performance: 12.691 1.891
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.122 0.123 99.6
62: (ns/day) (hour/ns)
62: Performance: 11.948 2.009
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (867 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.128 0.128 99.7
62: (ns/day) (hour/ns)
62: Performance: 11.431 2.100
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.109 0.109 99.6
62: (ns/day) (hour/ns)
62: Performance: 13.432 1.787
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.112 0.112 99.5
62: (ns/day) (hour/ns)
62: Performance: 13.100 1.832
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.126 0.126 99.5
62: (ns/day) (hour/ns)
62: Performance: 11.621 2.065
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.4-Raspbian-2021.4-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.140 0.140 99.7
62: (ns/day) (hour/ns)
62: Performance: 10.473 2.292
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>